623 lines
719 KiB
Plaintext
623 lines
719 KiB
Plaintext
Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene avsnp150 cosmic91 CLNALLELEID CLNDN CLNDISDB CLNREVSTAT CLNSIG 1000g2015aug_all 1000g2015aug_eas esp6500siv2_all ExAC_nontcga_ALL ExAC_nontcga_AFR ExAC_nontcga_AMR ExAC_nontcga_EAS ExAC_nontcga_FIN ExAC_nontcga_NFE ExAC_nontcga_OTH ExAC_nontcga_SAS gnomAD_genome_ALL gnomAD_genome_AFR gnomAD_genome_AMR gnomAD_genome_ASJ gnomAD_genome_EAS gnomAD_genome_FIN gnomAD_genome_NFE gnomAD_genome_OTH SIFT_score SIFT_converted_rankscore SIFT_pred LRT_score LRT_converted_rankscore LRT_pred MutationTaster_score MutationTaster_converted_rankscore MutationTaster_pred MutationAssessor_score MutationAssessor_score_rankscore MutationAssessor_pred FATHMM_score FATHMM_converted_rankscore FATHMM_pred PROVEAN_score PROVEAN_converted_rankscore PROVEAN_pred MetaSVM_score MetaSVM_rankscore MetaSVM_pred MetaLR_score MetaLR_rankscore MetaLR_pred M-CAP_score M-CAP_rankscore M-CAP_pred MutPred_score MutPred_rankscore fathmm-MKL_coding_score fathmm-MKL_coding_rankscore fathmm-MKL_coding_pred Eigen_coding_or_noncoding Eigen-raw Eigen-PC-raw GenoCanyon_score GenoCanyon_score_rankscore integrated_fitCons_score integrated_fitCons_score_rankscore integrated_confidence_value GERP++_RS GERP++_RS_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore phyloP20way_mammalian phyloP20way_mammalian_rankscore phastCons100way_vertebrate phastCons100way_vertebrate_rankscore phastCons20way_mammalian phastCons20way_mammalian_rankscore SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore Interpro_domain GTEx_V6p_gene GTEx_V6p_tissue cytoBand Otherinfo1 Otherinfo2 Otherinfo3 Otherinfo4 Otherinfo5 Otherinfo6 Otherinfo7 Otherinfo8 Otherinfo9 Otherinfo10 Otherinfo11 Otherinfo12 Otherinfo13 Otherinfo14
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chr1 11205058 11205058 C T exonic MTOR . synonymous SNV MTOR:NM_004958:exon33:c.4731G>A:p.A1577A rs1057079 ID=COSV63875443;OCCURENCE=2(breast),2(central_nervous_system),1(thyroid) 497979 Smith-Kingsmore_syndrome|not_specified|not_provided MONDO:MONDO:0014716,MedGen:C4225259,OMIM:616638,Orphanet:ORPHA457485|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.547524 0.8165 0.5459 0.6773 0.1562 0.7356 0.8226 0.7245 0.7331 0.7075 0.6509 0.5689 0.1535 0.7124 0.5530 0.8004 0.7093 0.7379 0.6735 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.22 1 386 2151 chr1 11205058 . C T 386 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2179;VD=2169;AF=0.9954;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20217;SOR=1.52302;LSEQ=CTGTAACTCTCTCCTGCCAT;RSEQ=GCAGTTAATTCAGCATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2179:2169:1258,911:0,0:0,2169:0.9954:0,2:38.8:1:34.9:1:1:0:60:2168:0.9959:0.0257:1.1 1/1:2151:2136:1174,962:1,0:1,2136:0.993:0,2:39.1:1:34.9:1:1:0:60:533:0.9939:0.0237:1.1
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chr1 11288758 11288758 G A exonic MTOR . synonymous SNV MTOR:NM_004958:exon19:c.2997C>T:p.N999N rs1064261 ID=COSV63873449;OCCURENCE=1(breast),1(thyroid),3(central_nervous_system) 1153195 Smith-Kingsmore_syndrome|not_specified|not_provided MONDO:MONDO:0014716,MedGen:C4225259,OMIM:616638,Orphanet:ORPHA457485|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.700479 0.9187 0.6176 0.7480 0.3823 0.8734 0.9188 0.7455 0.7340 0.7752 0.8283 0.6449 0.3858 0.8365 0.6126 0.9283 0.7467 0.7263 0.7157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.22 1 399 2672 chr1 11288758 . G A 399 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2820;VD=2814;AF=0.9979;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35616;SOR=1.40831;LSEQ=CCATCACAGACTCGAATGAC;RSEQ=TTAAGGAACGTGGGCATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2820:2814:1756,1058:0,1:1,2814:0.9979:0,2:38.7:1:34.9:1:0.3762:0:60:1406:0.9989:0.0337:1.2 1/1:2672:2664:1700,964:0,0:0,2664:0.997:0,2:39.3:1:34.9:1:1:0:60:5328:0.9978:0.0082:1.2
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chr1 11301714 11301714 A G exonic MTOR . synonymous SNV MTOR:NM_004958:exon10:c.1437T>C:p.D479D rs1135172 ID=COSV63873456;OCCURENCE=1(breast),2(central_nervous_system),1(thyroid) 498006 Smith-Kingsmore_syndrome|not_specified|not_provided MONDO:MONDO:0014716,MedGen:C4225259,OMIM:616638,Orphanet:ORPHA457485|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.639577 0.878 0.5853 0.7201 0.2879 0.8036 0.8797 0.7454 0.7337 0.7637 0.7681 0.6129 0.2871 0.7751 0.6126 0.8837 0.7487 0.7263 0.7070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.22 1 393 2682 chr1 11301714 . A G 393 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2731;VD=2716;AF=0.9945;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00005;SOR=3.08938;LSEQ=ATGCAAGTGAAGACTGTGGC;RSEQ=TCCACCTGCATTGCCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2731:2716:1409,1307:0,0:0,2716:0.9945:0,2:37.9:1:34.5:1:1:0:60:96:0.997:0.0326:1.1 1/1:2682:2637:1334,1303:3,0:3,2637:0.9832:0,2:38.7:1:34.6:1:0.24984:0:60:145.5:0.9872:0.0224:1.1
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chr1 11854457 11854457 G A exonic MTHFR . synonymous SNV MTHFR:NM_001330358:exon8:c.1428C>T:p.F476F,MTHFR:NM_005957:exon8:c.1305C>T:p.F435F rs4846051 . 177842 Homocystinuria_due_to_methylene_tetrahydrofolate_reductase_deficiency|Homocystinuria_due_to_MTHFR_deficiency|not_specified MONDO:MONDO:0009353,MedGen:C1856058,OMIM:236250,Orphanet:ORPHA395|MedGen:C4017062|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.902955 0.996 0.8905 0.9700 0.6844 0.9846 0.9994 1 0.9976 0.9942 0.9992 0.9091 0.6825 0.9809 0.9768 0.9988 1 0.9992 0.9867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.22 1 400 2730 chr1 11854457 . G A 400 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2832;VD=2822;AF=0.9965;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3821;SOR=1.24586;LSEQ=TCTCCCGAGAGGTAAAGAAC;RSEQ=AAGACTTCAAAGACACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2832:2822:1598,1224:1,0:1,2822:0.9965:0,2:39.1:1:34.9:1:1:0:60:2821:0.9968:0.0339:1.5 1/1:2730:2718:1496,1222:0,0:0,2718:0.9956:0,2:39:1:34.9:1:1:0:60:2717:0.996:0.0458:1.6
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chr1 11854476 11854476 T G exonic MTHFR . nonsynonymous SNV MTHFR:NM_001330358:exon8:c.1409A>C:p.E470A,MTHFR:NM_005957:exon8:c.1286A>C:p.E429A rs1801131 ID=COSV57171183;OCCURENCE=1(liver),1(large_intestine),4(haematopoietic_and_lymphoid_tissue),1(urinary_tract),10(soft_tissue),1(pancreas),1(skin),1(lung) 18560 Schizophrenia,_susceptibility_to|Gastrointestinal_stromal_tumor|Homocystinuria_due_to_methylene_tetrahydrofolate_reductase_deficiency|Neural_tube_defects,_folate-sensitive|MTHFR_deficiency,_thermolabile_type|Homocystinuria_due_to_MTHFR_deficiency|not_specified|not_provided .|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0009353,MedGen:C1856058,OMIM:236250,Orphanet:ORPHA395|MONDO:MONDO:0011120,MedGen:C1866558,OMIM:601634|MedGen:C1856059|MedGen:C4017062|MedGen:CN169374|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity|_other 0.249401 0.2192 0.2596 0.2949 0.1578 0.1546 0.2145 0.3128 0.3193 0.3170 0.4157 0.2590 0.1663 0.1838 0.2881 0.2255 0.3090 0.3074 0.2735 0.1 0.305 T 0.000 0.629 D 0.000 0.588 P 1.45 0.368 L -0.78 0.736 T -3.09 0.634 D -1.076 0.082 T 0.000 0.000 T . . . . . 0.961 0.671 D c -0.157 -0.061 1.000 0.747 0.732 0.924 0 4.74 0.596 3.756 0.547 1.061 0.807 0.968 0.339 0.914 0.390 13.742 0.622 . ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000011021.17|ENSG00000177000.6|ENSG00000177000.6|ENSG00000242349.1|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000011021.17|ENSG00000242349.1|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000011021.17|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6|ENSG00000011021.17|ENSG00000177000.6|ENSG00000177000.6|ENSG00000177000.6 Adipose_Subcutaneous|Adipose_Visceral_Omentum|Artery_Aorta|Artery_Tibial|Artery_Tibial|Brain_Caudate_basal_ganglia|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Nucleus_accumbens_basal_ganglia|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Transverse|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Lung|Muscle_Skeletal|Nerve_Tibial|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Thyroid|Whole_Blood 1p36.22 0.5 360 2736 chr1 11854476 . T G 360 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2793;VD=1332;AF=0.4769;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02999;SOR=0.90244;LSEQ=CGAAGACTTCAAAGACACTT;RSEQ=CTTCACTGGTCAGCTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2793:1332:699,633:793,665:1458,1332:0.4769:2,2:38.8:1:34.5:1:0.32327:1.07986:60:189.286:0.4761:0.0208:2 1/0:2736:1375:728,647:694,662:1356,1375:0.5026:2,2:37.8:1:34.6:1:0.35822:1.07:60:136.5:0.5022:0.0172:1.9
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chr1 11856378 11856378 G A exonic MTHFR . nonsynonymous SNV MTHFR:NM_001330358:exon5:c.788C>T:p.A263V,MTHFR:NM_005957:exon5:c.665C>T:p.A222V rs1801133 ID=COSV64876755;OCCURENCE=1(breast),3(haematopoietic_and_lymphoid_tissue),2(stomach),1(urinary_tract),24(soft_tissue),1(prostate),1(lung) 18559 methotrexate_response_-_Metabolism/PK|Neoplasm_of_stomach|Gastrointestinal_stromal_tumor|Thrombophilia_due_to_thrombin_defect|Homocystinuria_due_to_methylene_tetrahydrofolate_reductase_deficiency|Neural_tube_defects,_folate-sensitive|methotrexate_response_-_Toxicity|MTHFR_deficiency,_thermolabile_type|Homocystinuria_due_to_MTHFR_deficiency|not_specified|not_provided .|Human_Phenotype_Ontology:HP:0006753,MONDO:MONDO:0021085,MedGen:C0038356,SNOMED_CT:126824007|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0008559,MedGen:C3160733,OMIM:188050|MONDO:MONDO:0009353,MedGen:C1856058,OMIM:236250,Orphanet:ORPHA395|MONDO:MONDO:0011120,MedGen:C1866558,OMIM:601634|MONDO:MONDO:0034212,MedGen:C0568062,Orphanet:ORPHA565782,SNOMED_CT:290680001|MedGen:C1856059|MedGen:C4017062|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel drug_response 0.245407 0.2956 0.2706 0.3013 0.1110 0.5170 0.3118 0.2227 0.3449 0.3055 0.1407 0.2572 0.1131 0.4845 0.4470 0.2866 0.2351 0.3265 0.2633 0.002 0.721 D 0.000 0.843 D 0.000 0.588 P 2.965 0.855 M -4.03 0.964 D -3.76 0.712 D -1.455 0.000 T 0.000 0.000 T . . . . . 0.980 0.783 D c 0.739 0.658 1.0 0.983 0.722 0.854 0 5.08 0.682 9.137 0.937 1.048 0.713 1.000 0.715 0.530 0.276 17.432 0.874 FAD-linked oxidoreductase-like ENSG00000242349.1|ENSG00000242349.1|ENSG00000242349.1|ENSG00000242349.1|ENSG00000242349.1|ENSG00000242349.1|ENSG00000177000.6|ENSG00000242349.1|ENSG00000177000.6|ENSG00000116688.12 Adipose_Subcutaneous|Artery_Tibial|Brain_Cerebellum|Cells_Transformed_fibroblasts|Lung|Muscle_Skeletal|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Thyroid|Whole_Blood 1p36.22 0.5 340 2006 chr1 11856378 . G A 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1958;VD=956;AF=0.4883;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46967;SOR=1.00688;LSEQ=GCTGCGTGATGATGAAATCG;RSEQ=CTCCCGCAGACACCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1958:956:491,465:500,499:999,956:0.4883:2,2:40.8:1:34.3:1:0.58717:1.05:60:135.571:0.4897:0.0133:1.1 0/1:2006:976:511,465:503,525:1028,976:0.4865:2,2:40.8:1:34.3:1:0.12876:1.15:60:87.727:0.4891:0.009:1.1
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chr1 17371411 17371411 - A intron SDHB NM_003000:exon2:c.73-28->T . . rs745905902 ID=COSV100973532;OCCURENCE=1(stomach) . . . . . . . . 0.0003 0.0004 0.0001 0.0005 0 0.0004 0.0016 0.0003 3.399e-05 0 0 0 0 0 7.046e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.13 0.5 179 1523 chr1 17371411 . G GA 179 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1555;VD=34;AF=0.0219;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.46508;SOR=0.95035;LSEQ=TTTTTAAAGTTCACAAAAAG;RSEQ=AAAAAAAAATTAGAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1555:34:9,25:619,745:1364,34:0.0219:2,2:43.4:1:34.6:1:0.03518:2.30664:60:68:0.0256:0.0006:0.4 0/1:1523:35:17,17:628,780:1408,35:0.023:2,2:41.1:1:35:1:0.60175:1.24:60:70:0.0255:0.002:0.5
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chr1 17380497 17380497 G T exonic SDHB . synonymous SNV SDHB:NM_003000:exon1:c.18C>A:p.A6A rs2746462 . 53808 Pheochromocytoma|Gastrointestinal_stromal_tumor|Paragangliomas_4|Carney-Stratakis_syndrome|Hereditary_cancer-predisposing_syndrome|Hereditary_Paraganglioma-Pheochromocytoma_Syndromes|Mitochondrial_complex_2_deficiency,_nuclear_type_4|not_specified|not_provided Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0007273,MedGen:C1861848,OMIM:115310|MONDO:MONDO:0011740,MedGen:C1847319,OMIM:606864,Orphanet:ORPHA97286|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072|MONDO:MONDO:0030974,MedGen:C5543176,OMIM:619224|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.957069 0.996 0.9515 0.9725 0.9092 0.9876 0.9987 0.9812 0.9697 0.9792 0.9877 0.9577 0.9069 0.9690 0.9371 0.9994 0.9823 0.9755 0.9785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.13 1 371 1686 chr1 17380497 . G T 371 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1782;VD=1766;AF=0.991;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56201;SOR=0.9908;LSEQ=AACCGGCGCCTCAAGGAGAG;RSEQ=GCGACCACCGCCGCCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1782:1766:943,823:0,0:0,1766:0.991:0,2:40.9:1:34.4:1:1:0:60:97.111:0.9937:0.0213:1.1 1/1:1686:1671:846,825:0,1:1,1671:0.9911:0,2:41.2:1:34.4:1:0.49402:0:60:138.25:0.994:0.0071:1.1
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chr1 27022838 27022838 G - intron ARID1A NM_139135:c.-57del-;NM_006015:c.-57del- . . rs888239148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.25 140 1528 chr1 27022837 . AG A 140 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=1638;VD=11;AF=0.0067;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16984;SOR=0.639;LSEQ=GGGCCCCGGGGCGGGGTGGG;RSEQ=GGGGGGAGAAGACGAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1638:11:6,5:1100,527:1627,11:0.0067:2,2:38:1:34.6:1:0.35028:1.73881:60:22:0.0068:0.0006:0.2 0/1:1528:16:13,3:1026,486:1512,16:0.0105:2,2:42.4:1:35:1:0.29624:2.05:60:32:0.0106:0.0007:0.2
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chr1 27022940 27022942 CCG - exonic ARID1A . nonframeshift deletion ARID1A:NM_006015:exon1:c.46_48del:p.P21del,ARID1A:NM_139135:exon1:c.46_48del:p.P21del rs748085214 ID=COSV61387765;OCCURENCE=1(large_intestine),1(stomach) 696661 not_provided MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Likely_benign . . 0.0134 0.0502 0.0833 0 0 . 0.0882 0 0.0405 3.551e-05 0 0.0015 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.5 200 1903 chr1 27022939 . CCCG C 200 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2060;VD=47;AF=0.0228;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.13386;SOR=0.78455;LSEQ=GCCGCCAGCAGCCTGGGCAA;RSEQ=CCGCCGCCGCCGCCCTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2060:47:31,16:1309,702:2011,47:0.0228:2,2:38.5:1:35:1:1:1.04:60:94:0.0229:0.0029:0.3 0/1:1903:55:42,13:1197,648:1845,55:0.0289:2,2:38.6:1:34.7:1:0.08536:1.75:60:110:0.0291:0.0037:0.5
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chr1 27023008 27023010 GGC - exonic ARID1A . nonframeshift deletion ARID1A:NM_006015:exon1:c.114_116del:p.A45del,ARID1A:NM_139135:exon1:c.114_116del:p.A45del rs769912952 ID=COSV61373654;OCCURENCE=1(large_intestine),1(ovary),1(haematopoietic_and_lymphoid_tissue),1(lung) 582375 not_provided MedGen:CN517202 no_assertion_criteria_provided Uncertain_significance . . . 0 . . . . . . 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.5 175 2044 chr1 27023007 . AGGC A 175 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2247;VD=32;AF=0.0142;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.44973;SOR=0.93816;LSEQ=GCGGGAGGAGGCGGGGGGCG;RSEQ=GGCGGCGGCGGCAGCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2247:32:22,10:1444,766:2210,32:0.0142:2,2:41.2:1:35:1:0.85184:1.17:60:64:0.0143:0.0013:0.2 0/1:2044:31:19,12:1332,674:2006,31:0.0152:2,2:45.5:1:34.6:1:0.56836:1.248:60:62:0.0152:0:0.4
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chr1 27023141 27023143 GGC - exonic ARID1A . nonframeshift deletion ARID1A:NM_006015:exon1:c.247_249del:p.G87del,ARID1A:NM_139135:exon1:c.247_249del:p.G87del . ID=COSV104411784;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.25 166 2512 chr1 27023140 . TGGC T 166 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=2707;VD=25;AF=0.0092;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.24599;SOR=0.79814;LSEQ=GGGGCCGAGAGCAATGGGGG;RSEQ=GGCGGCGGCGGAGCCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2707:25:18,7:1786,893:2679,25:0.0092:2,2:44.7:1:35:0:0.67333:1.29:60:50:0.0093:0:0.6 0/1:2512:29:15,14:1690,793:2483,29:0.0115:2,2:50.3:1:34.2:1:0.07181:1.98854:60:28:0.0112:0:0.4
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chr1 27100182 27100184 GCA - exonic ARID1A . nonframeshift deletion ARID1A:NM_006015:exon16:c.3978_3980del:p.Q1334del,ARID1A:NM_139135:exon16:c.3978_3980del:p.Q1334del rs374564889 ID=COSV61371125;OCCURENCE=1(salivary_gland),3(breast),4(large_intestine),2(bone),3(NS),1(haematopoietic_and_lymphoid_tissue),2(stomach),1(kidney),1(prostate),1(lung),2(upper_aerodigestive_tract),1(endometrium) 707303 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.0063 0.0074 0.0089 0.0067 0.0045 0.0061 0.0132 0.0049 3.242e-05 0 0 0 0 0 0 0.0010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.5 242 3170 chr1 27100181 . CGCA C 242 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3099;VD=124;AF=0.04;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=0.24003;SOR=1.10724;LSEQ=TTCTCCTAGCCGCTACCCCC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3099:124:75,49:1724,1234:2958,124:0.04:2,2:42.5:1:34.8:1:0.64332:1.10:60:248:0.0408:0.0048:0.1 0/1:3170:115:67,48:1756,1280:3036,115:0.0363:2,2:41.6:1:34.9:1:1:1.02:60:230:0.0367:0.0025:0.2
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chr1 27105676 27105678 GAA - exonic ARID1A . nonframeshift deletion ARID1A:NM_006015:exon20:c.5287_5289del:p.E1767del,ARID1A:NM_139135:exon20:c.4636_4638del:p.E1550del rs760362729 ID=COSV61382756;OCCURENCE=1(soft_tissue) 1218716 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . 0.0030 0.0002 0.0001 8.953e-05 0.0001 0.0002 5.673e-05 0 0.0007 9.689e-05 0.0002 0 0 0.0006 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.25 162 2415 chr1 27105675 . GGAA G 162 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2533;VD=26;AF=0.0103;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02349;SOR=2.07648;LSEQ=CCAGCTCCCATGGAGGGTGG;RSEQ=GAAGAAGAAGAACTTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2533:26:17,9:1639,867:2506,26:0.0103:2,2:41.2:1:34.6:1:1:1.00081:60:52:0.0105:0.0004:0 0/0:2415:12:11,1:1556,846:2402,12:0.005:2,2:28.5:1:35:1:0.06715:5.98:60:24:0.0051:0.0017:0.2
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chr1 27107264 27107264 C - UTR3 ARID1A NM_139135:c.*17delC;NM_006015:c.*17delC . . rs745390232 . . . . . . . . 0.0154 0.0013 0.0050 0.0009 0.0012 0 0.0007 0.0018 0.0029 0.0010 0.0030 0 0 0.0019 0 6.891e-05 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p36.11 0.5 222 1832 chr1 27107263 . TC T 222 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1746;VD=74;AF=0.0424;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28154;SOR=0.89858;LSEQ=CATGACAGCCGTGGGACACC;RSEQ=CCCCCCCCGTGTGTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1746:74:22,52:715,955:1670,74:0.0424:2,2:45.5:1:34.7:1:0.02993:1.76908:60:148:0.043:0.0034:0.2 0/1:1832:86:28,58:731,1013:1744,86:0.0469:2,2:39.8:1:34.7:1:0.09302:1.49446:60:172:0.0476:0.0027:0.1
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chr1 45796269 45796269 G C intron MUTYH NM_001293195:exon16:c.1393-40C>G;NM_001293191:exon15:c.1426-40C>G;NM_001128425:exon15:c.1477-40C>G;NM_001293196:exon15:c.1117-40C>G;NM_001048171:exon15:c.1435-40C>G;NM_012222:exon15:c.1468-40C>G;NM_001293190:exon15:c.1438-40C>G;NM_001293192:exon15:c.1117-40C>G;NM_001350651:exon14:c.1048-40C>G;NM_001350650:exon14:c.1048-40C>G;NM_001048173:exon15:c.1393-40C>G;NM_001048174:exon15:c.1393-40C>G;NM_001048172:exon15:c.1396-40C>G . . rs3219493 . 432989 not_provided MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.935304 0.9137 0.9263 0.9254 0.9583 0.9568 0.8885 0.9757 0.9160 0.9327 0.9158 0.9359 0.9563 0.9379 0.8907 0.8907 0.9731 0.921 0.9348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p34.1 1 369 1930 chr1 45796269 . G C 369 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1909;VD=1901;AF=0.9958;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28335;SOR=0.61729;LSEQ=GGTGAGGGCTGGCACTTTTT;RSEQ=CAAAAGAGATAAACCGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1909:1901:843,1058:0,0:0,1901:0.9958:0,2:42.9:1:33.6:1:1:0:60:43.209:0.9979:0:1.2 1/1:1930:1925:836,1089:0,2:2,1925:0.9974:0,2:41.9:1:33.9:1:0.5085:0:60:47.125:0.9995:0.0311:1.2
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chr1 45797505 45797505 C G exonic MUTYH . nonsynonymous SNV MUTYH:NM_001350650:exon11:c.585G>C:p.Q195H,MUTYH:NM_001350651:exon11:c.585G>C:p.Q195H,MUTYH:NM_001048171:exon12:c.972G>C:p.Q324H,MUTYH:NM_001048172:exon12:c.933G>C:p.Q311H,MUTYH:NM_001048173:exon12:c.930G>C:p.Q310H,MUTYH:NM_001048174:exon12:c.930G>C:p.Q310H,MUTYH:NM_001128425:exon12:c.1014G>C:p.Q338H,MUTYH:NM_001293190:exon12:c.975G>C:p.Q325H,MUTYH:NM_001293191:exon12:c.963G>C:p.Q321H,MUTYH:NM_001293192:exon12:c.654G>C:p.Q218H,MUTYH:NM_001293196:exon12:c.654G>C:p.Q218H,MUTYH:NM_012222:exon12:c.1005G>C:p.Q335H,MUTYH:NM_001293195:exon13:c.930G>C:p.Q310H rs3219489 ID=COSV58343790;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),19(soft_tissue),1(lung) 50206 Carcinoma_of_colon|MYH-associated_polyposis|Hereditary_cancer-predisposing_syndrome|Familial_multiple_polyposis_syndrome|not_specified|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0012041,MedGen:C3272841,OMIM:608456,Orphanet:ORPHA247798|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021055,MedGen:C0032580,OMIM:PS175100,Orphanet:ORPHA733,SNOMED_CT:72900001|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.313498 0.3909 0.2541 0.3016 0.2877 0.5352 0.4292 0.2429 0.2632 0.2965 0.2444 0.2584 0.2696 0.4353 0.3013 0.4143 0.2278 0.2327 0.2382 0.168 0.284 T 0.038 0.243 N 0.743 0.588 P 2.665 0.782 M 3.23 0.229 T -1.03 0.270 N -0.933 0.437 T 0.000 0.000 T . . . . . 0.147 0.184 N c -0.583 -0.613 0.998 0.361 0.732 0.924 0 1.26 0.204 -0.265 0.086 0.935 0.490 0.000 0.063 0.732 0.317 2.473 0.043 DNA glycosylase|Helix-turn-helix, base-excision DNA repair, C-terminal ENSG00000132763.10|ENSG00000117450.9|ENSG00000132763.10|ENSG00000117450.9|ENSG00000132781.13|ENSG00000132763.10|ENSG00000117450.9|ENSG00000236624.4|ENSG00000132763.10|ENSG00000132763.10|ENSG00000236624.4|ENSG00000117450.9|ENSG00000236624.4|ENSG00000132763.10|ENSG00000159596.6|ENSG00000236624.4|ENSG00000070759.12|ENSG00000132763.10|ENSG00000117450.9|ENSG00000070759.12|ENSG00000236624.4 Adipose_Subcutaneous|Adipose_Subcutaneous|Artery_Tibial|Artery_Tibial|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Left_Ventricle|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Testis|Thyroid|Thyroid|Whole_Blood|Whole_Blood 1p34.1 0.5 364 2764 chr1 45797505 . C G 364 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2900;VD=1441;AF=0.4969;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20242;SOR=0.95531;LSEQ=GGAGGCAGGCACAGGTGGCA;RSEQ=TGTCCAGTGTTGGGAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2900:1441:769,672:838,612:1450,1441:0.4969:2,2:38.7:1:34.7:1:0.01835:1.19648:60:479.333:0.5012:0.0128:1.1 1/0:2764:1405:798,607:749,603:1352,1405:0.5083:2,2:38.9:1:34.6:1:0.466:1.06:60:155.111:0.5093:0.013:1.1
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chr1 45798555 45798555 T C intron MUTYH NM_001293195:exon7:c.420+35A>G;NM_001293195:exon8:c.421-49A>G;NM_001293191:exon6:c.453+35A>G;NM_001293191:exon7:c.454-49A>G;NM_001128425:exon6:c.504+35A>G;NM_001128425:exon7:c.505-49A>G;NM_001293196:exon6:c.144+35A>G;NM_001293196:exon7:c.145-49A>G;NM_001048171:exon6:c.462+35A>G;NM_001048171:exon7:c.463-49A>G;NM_012222:exon6:c.495+35A>G;NM_012222:exon7:c.496-49A>G;NM_001293190:exon6:c.465+35A>G;NM_001293190:exon7:c.466-49A>G;NM_001293192:exon6:c.144+35A>G;NM_001293192:exon7:c.145-49A>G;NM_001350651:exon5:c.75+35A>G;NM_001350651:exon6:c.76-49A>G;NM_001350650:exon5:c.75+35A>G;NM_001350650:exon6:c.76-49A>G;NM_001048173:exon6:c.420+35A>G;NM_001048173:exon7:c.421-49A>G;NM_001048174:exon6:c.420+35A>G;NM_001048174:exon7:c.421-49A>G;NM_001048172:exon6:c.423+35A>G;NM_001048172:exon7:c.424-49A>G . . rs3219487 ID=COSV58343750;OCCURENCE=1(central_nervous_system),1(biliary_tract) 249965 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.937101 0.9137 0.9303 0.9266 0.9651 0.9569 0.8835 0.9764 0.9172 0.9395 0.9160 0.9393 0.9665 0.9390 0.8940 0.8926 0.9731 0.9218 0.9357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p34.1 1 390 2483 chr1 45798555 . T C 390 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2425;VD=2419;AF=0.9975;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51734;SOR=1.13978;LSEQ=TCACCCGTCAGTCCCTCTAT;RSEQ=GTTCCTATTTCCCCTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2425:2419:1235,1184:0,2:2,2419:0.9975:0,2:40.1:1:34.6:1:0.23988:0:60:171.786:0.9979:0.0082:1.1 1/1:2483:2476:1237,1239:2,0:2,2476:0.9972:0,2:38.8:1:34.6:1:0.4998:0:60:189.462:0.998:0.0169:1.1
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chr1 46726876 46726876 - T intronic RAD54L . . . rs750795604 ID=COSV64335641;OCCURENCE=5(biliary_tract) . . . . . . . . . . . . . . . . 0.0187 0.0171 0.0445 0.0304 0.0033 0.0794 0.0133 0.0297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p34.1 0.5 287 2000 chr1 46726876 . G GT 287 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1917;VD=304;AF=0.1586;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.48616;SOR=0.99315;LSEQ=ACTGTCTAATTGTTTTTTTT;RSEQ=TTTTTTTTTTTTTCAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1917:304:176,128:787,428:1215,304:0.1586:2,2:43.6:1:34.8:1:0.02807:1.337:60:608:0.2671:0:0.2 0/1:2000:319:195,124:792,474:1266,319:0.1595:2,2:42.9:1:34.6:1:0.65127:1.06247:60:158.5:0.255:0:0.2
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chr1 65306996 65306996 - T exonic JAK1 . frameshift insertion JAK1:NM_001321852:exon19:c.2580dupA:p.P861Tfs*4,JAK1:NM_001321856:exon19:c.2580dupA:p.P861Tfs*4,JAK1:NM_001321857:exon19:c.2577dupA:p.P860Tfs*4,JAK1:NM_002227:exon19:c.2580dupA:p.P861Tfs*4,JAK1:NM_001320923:exon20:c.2580dupA:p.P861Tfs*4,JAK1:NM_001321854:exon20:c.2580dupA:p.P861Tfs*4,JAK1:NM_001321855:exon20:c.2580dupA:p.P861Tfs*4,JAK1:NM_001321853:exon21:c.2580dupA:p.P861Tfs*4 . ID=COSV61088749;OCCURENCE=1(breast),3(large_intestine),2(endometrium) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.25 160 2157 chr1 65306996 . G GT 160 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=2268;VD=24;AF=0.0106;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27078;SOR=1.27087;LSEQ=GGGGTCCACTTCAGTTGCTG;RSEQ=TTTTTTTTCTGAAACAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2268:24:16,7:1164,878:2042,24:0.0106:2,2:28.9:1:35:1:0.29072:1.72:60:48:0.012:0.0013:0.3 0/0:2157:18:12,6:1177,861:2038,18:0.0083:2,2:37.7:1:34.7:1:0.48412:1.46:60:36:0.0089:0.0019:0.3
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chr1 65311214 65311214 G C exonic JAK1 . synonymous SNV JAK1:NM_001321852:exon15:c.2097C>G:p.A699A,JAK1:NM_001321856:exon15:c.2097C>G:p.A699A,JAK1:NM_001321857:exon15:c.2094C>G:p.A698A,JAK1:NM_002227:exon15:c.2097C>G:p.A699A,JAK1:NM_001320923:exon16:c.2097C>G:p.A699A,JAK1:NM_001321854:exon16:c.2097C>G:p.A699A,JAK1:NM_001321855:exon16:c.2097C>G:p.A699A,JAK1:NM_001321853:exon17:c.2097C>G:p.A699A rs3737139 ID=COSV61087128;OCCURENCE=1(breast),3(soft_tissue),1(lung) 1153652 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.038738 0.0069 0.0446 0.0620 0.0089 0.1724 0.0093 0.0448 0.0571 0.0536 0.0627 0.0469 0.0114 0.1348 0.0298 0.0136 0.0481 0.0657 0.0571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.5 350 2274 chr1 65311214 . G C 350 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2315;VD=1125;AF=0.486;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39505;SOR=0.98268;LSEQ=ACCAAGTAGCTCAGGGCACT;RSEQ=GCCAGCTGTTTGGCAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2315:1125:707,418:751,434:1185,1125:0.486:2,2:39.4:1:34.6:1:0.79592:1.02307:60:224:0.4859:0.016:1.1 0/1:2274:1115:704,411:714,438:1152,1115:0.4903:2,2:38.3:1:34.6:1:0.5729:1.05:60:138.375:0.4896:0.0123:1.1
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chr1 65321250 65321250 G A exonic JAK1 . synonymous SNV JAK1:NM_001321852:exon11:c.1590C>T:p.I530I,JAK1:NM_001321856:exon11:c.1590C>T:p.I530I,JAK1:NM_001321857:exon11:c.1587C>T:p.I529I,JAK1:NM_002227:exon11:c.1590C>T:p.I530I,JAK1:NM_001320923:exon12:c.1590C>T:p.I530I,JAK1:NM_001321854:exon12:c.1590C>T:p.I530I,JAK1:NM_001321855:exon12:c.1590C>T:p.I530I,JAK1:NM_001321853:exon13:c.1590C>T:p.I530I rs2230586 ID=COSV61087133;OCCURENCE=1(breast),3(soft_tissue),1(skin),1(lung) 1153655 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.038738 0.0069 0.0442 0.0621 0.0088 0.1728 0.0093 0.0459 0.0570 0.0543 0.0632 0.0471 0.0113 0.1360 0.0298 0.0136 0.0481 0.0660 0.0562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.5 348 2122 chr1 65321250 . G A 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2161;VD=1060;AF=0.4905;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36859;SOR=1.02264;LSEQ=CTGATGTTATCCGTGCGCAG;RSEQ=ATCTGCTTCTTGAGGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2161:1060:597,463:631,466:1097,1060:0.4905:2,2:39.3:1:34.7:1:0.60177:1.05009:60:264:0.493:0.0134:1.2 0/1:2122:1029:603,426:638,449:1087,1029:0.4849:2,2:41.3:1:34.8:1:1:1.00384:60:1028:0.4902:0.0094:1.2
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chr1 65321388 65321388 G A intron JAK1 NM_001320923:exon12:c.1459-7C>T;NM_001321856:exon11:c.1459-7C>T;NM_001321855:exon12:c.1459-7C>T;NM_001321852:exon11:c.1459-7C>T;NM_001321853:exon13:c.1459-7C>T;NM_002227:exon11:c.1459-7C>T;NM_001321857:exon11:c.1459-10C>T;NM_001321854:exon12:c.1459-7C>T . . rs310229 ID=COSV61087137;OCCURENCE=2(breast),2(haematopoietic_and_lymphoid_tissue),12(soft_tissue),1(lung) 1153656 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.402556 0.3065 0.3801 0.3590 0.5870 0.5423 0.3236 0.3301 0.3076 0.3493 0.3119 0.4079 0.5930 0.4665 0.3974 0.3180 0.3254 0.3296 0.3535 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.5 329 1509 chr1 65321388 . G A 329 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1439;VD=643;AF=0.4468;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2497;SOR=0.94867;LSEQ=GCACCCTGCACCTGCTATTC;RSEQ=GGAAATGACCAGAAATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1439:643:242,401:317,477:794,643:0.4468:2,2:38.1:1:34.9:1:0.3844:1.10113:60:642:0.4502:0.025:1.9 0/1:1509:694:266,428:351,461:812,694:0.4599:2,2:40.8:1:34.9:1:0.05847:1.22492:60:1388:0.463:0.0219:1.9
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chr1 65325970 65325970 C T intron JAK1 NM_001320923:exon10:c.1177-25G>A;NM_001321856:exon9:c.1177-25G>A;NM_001321855:exon10:c.1177-25G>A;NM_001321852:exon9:c.1177-25G>A;NM_001321853:exon11:c.1177-25G>A;NM_002227:exon9:c.1177-25G>A;NM_001321857:exon9:c.1177-25G>A;NM_001321854:exon10:c.1177-25G>A . . rs310224 ID=COSV61087694;OCCURENCE=1(breast),1(haematopoietic_and_lymphoid_tissue),12(soft_tissue),2(lung) . . . . . 0.404153 0.3065 0.3827 0.3587 0.5916 0.5383 0.3203 0.3229 0.3023 0.3419 0.3234 0.4097 0.5998 0.4688 0.3974 0.3168 0.3254 0.3295 0.3532 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.5 333 1593 chr1 65325970 . C T 333 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1620;VD=760;AF=0.4691;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3786;SOR=0.97594;LSEQ=TGAGAGAGAAGAAATTCCCA;RSEQ=GGTTACATCATGTCTCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1620:760:241,519:300,559:859,760:0.4691:2,2:41.2:1:34.9:1:0.18692:1.15563:60:1520:0.472:0.0117:1.1 0/1:1593:757:234,523:285,546:831,757:0.4752:2,2:40.3:1:34.9:1:0.16376:1.16653:60:756:0.4779:0.0157:1.1
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chr1 65330682 65330682 G A intron JAK1 NM_001320923:exon9:c.991-27C>T;NM_001321856:exon8:c.991-27C>T;NM_001321855:exon9:c.991-27C>T;NM_001321852:exon8:c.991-27C>T;NM_001321853:exon10:c.991-27C>T;NM_002227:exon8:c.991-27C>T;NM_001321857:exon8:c.991-27C>T;NM_001321854:exon9:c.991-27C>T . . rs2256298 ID=COSV61087701;OCCURENCE=2(breast),1(oesophagus),2(haematopoietic_and_lymphoid_tissue),12(soft_tissue) . . . . . 0.367212 0.3065 0.3299 0.2999 0.5720 0.4792 0.3252 0.2375 0.2411 0.2654 0.2415 0.3537 0.5803 0.4081 0.2748 0.3137 0.2431 0.2560 0.2730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.5 318 1100 chr1 65330682 . G A 318 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1046;VD=515;AF=0.4924;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18395;SOR=0.92175;LSEQ=AGATACATAAAAGGGACAGG;RSEQ=TTAAGTTGCTTTCTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1046:515:188,327:179,351:530,515:0.4924:2,2:38.5:1:34.9:1:0.36476:1.13:60:1030:0.4985:0.0115:1.1 1/0:1100:564:196,368:187,349:536,564:0.5127:2,2:40.4:1:34.9:1:1:1.00602:60:563:0.5165:0.0082:1.1
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chr1 65335095 65335095 T C exonic JAK1 . synonymous SNV JAK1:NM_001321852:exon6:c.546A>G:p.G182G,JAK1:NM_001321856:exon6:c.546A>G:p.G182G,JAK1:NM_001321857:exon6:c.546A>G:p.G182G,JAK1:NM_002227:exon6:c.546A>G:p.G182G,JAK1:NM_001320923:exon7:c.546A>G:p.G182G,JAK1:NM_001321854:exon7:c.546A>G:p.G182G,JAK1:NM_001321855:exon7:c.546A>G:p.G182G,JAK1:NM_001321853:exon8:c.546A>G:p.G182G rs11585932 ID=COSV61087144;OCCURENCE=1(breast),3(soft_tissue),2(lung) 1153661 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0351438 0.0069 0.0446 0.0600 0.0087 0.1723 0.0093 0.0448 0.0569 0.0522 0.0508 0.0469 0.0112 0.1343 0.0298 0.0136 0.0479 0.0660 0.0540 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p31.3 0.5 353 2350 chr1 65335095 . T C 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2402;VD=1232;AF=0.5129;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.31584;SOR=1.02995;LSEQ=CACTCGTTCTCAATATCATG;RSEQ=CCATCCTGCTCGGTCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2402:1232:601,631:577,586:1163,1232:0.5129:2,2:39:1:34.4:1:0.71288:1.03379:60:81.133:0.5113:0.0279:1.1 1/0:2350:1188:568,620:546,610:1156,1188:0.5055:2,2:39.7:1:34.3:1:0.804:1.02:60:83.857:0.5043:0.0136:1.1
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chr1 97981395 97981395 T C exonic DPYD . nonsynonymous SNV DPYD:NM_000110:exon13:c.1627A>G:p.I543V rs1801159 ID=COSV64593269;OCCURENCE=1(liver),1(large_intestine),1(stomach),2(haematopoietic_and_lymphoid_tissue) 105969 capecitabine_response_-_Toxicity|fluorouracil_response_-_Toxicity|Dihydropyrimidine_dehydrogenase_deficiency|not_specified|not_provided .|.|MONDO:MONDO:0010130,MedGen:C1959620,OMIM:274270,Orphanet:ORPHA1675|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel drug_response 0.184904 0.2659 0.1836 0.1915 0.1574 0.3127 0.2531 0.1655 0.1960 0.1859 0.0952 0.1754 0.1552 0.2608 0.21 0.2427 0.1556 0.1802 0.1612 0.111 0.290 T 0.007 0.314 N 1.000 0.197 P 0.49 0.133 N -0.8 0.739 T 0.73 0.021 N -1.011 0.266 T 0.053 0.225 T . . . . . 0.809 0.401 D c -1.000 -0.919 0.007 0.115 0.693 0.558 0 -3.13 0.049 1.397 0.339 -0.169 0.106 0.994 0.380 0.975 0.474 9.702 0.392 Aldolase-type TIM barrel|Dihydroorotate dehydrogenase domain . . 1p21.3 0.5 340 1791 chr1 97981395 . T C 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1729;VD=898;AF=0.5194;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49758;SOR=1.00269;LSEQ=AGCAAGACCAAAAGGATTTA;RSEQ=AAACTTCAATCCGGCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1729:898:503,395:492,335:827,898:0.5194:2,2:39.1:1:34.6:1:0.15721:1.15322:60:223.5:0.5195:0.0278:1.1 1/0:1791:929:559,370:550,311:861,929:0.5187:2,2:38.5:1:34.5:1:0.10818:1.17045:60:131.714:0.5177:0.0184:1.1
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chr1 97981421 97981421 C T exonic DPYD . nonsynonymous SNV DPYD:NM_000110:exon13:c.1601G>A:p.S534N rs1801158 ID=COSV64597757;OCCURENCE=2(soft_tissue) 105971 capecitabine_response_-_Toxicity|fluorouracil_response_-_Toxicity|Dihydropyrimidine_dehydrogenase_deficiency|not_specified|not_provided .|.|MONDO:MONDO:0010130,MedGen:C1959620,OMIM:274270,Orphanet:ORPHA1675|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel drug_response 0.00958466 . 0.0149 0.0136 0.0031 0.0094 0 0.0140 0.0196 0.0130 0.0087 0.0114 0.0036 0.0119 0.0331 0.0006 0.0126 0.0161 0.0143 0.007 0.599 D 0.000 0.843 D 1.000 0.588 D 2.5 0.730 M -1.02 0.763 T -2.72 0.579 D 0.311 0.877 D 0.605 0.860 D . . . . . 0.962 0.678 D c 0.705 0.633 0.998 0.367 0.693 0.558 0 5.2 0.716 5.711 0.678 0.031 0.150 1.000 0.715 0.857 0.358 19.097 0.932 Aldolase-type TIM barrel|Dihydroorotate dehydrogenase domain . . 1p21.3 0.5 332 1524 chr1 97981421 . C T 332 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1484;VD=703;AF=0.4737;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34547;SOR=0.9688;LSEQ=TCAATCCGGCCATTTCTACA;RSEQ=TAATGTCCACCAGATCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1484:703:374,329:397,383:780,703:0.4737:2,2:40.7:1:34.9:1:0.37689:1.10:60:1406:0.4766:0.0135:1.1 0/1:1524:734:412,322:429,361:790,734:0.4816:2,2:41.9:1:34.9:1:0.50283:1.08:60:1468:0.4851:0.0112:1.1
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chr1 98348885 98348885 G A exonic DPYD . nonsynonymous SNV DPYD:NM_000110:exon2:c.85C>T:p.R29C,DPYD:NM_001160301:exon2:c.85C>T:p.R29C rs1801265 ID=COSV60076627;OCCURENCE=1(skin) 106000 Dihydropyrimidine_dehydrogenase_deficiency|not_provided MONDO:MONDO:0010130,MedGen:C1959620,OMIM:274270,Orphanet:ORPHA1675|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.739816 0.9137 0.7159 0.7651 0.5832 0.7942 0.9279 0.7035 0.7794 0.7767 0.7452 0.7199 0.5991 0.7769 0.8642 0.9284 0.7140 0.7626 0.7352 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1p21.3 1 373 1571 chr1 98348885 . G A 373 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1696;VD=1688;AF=0.9953;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34446;SOR=1.35157;LSEQ=TTTCTTGGCCGAAGTGGAAC;RSEQ=CAGAGTTGCATGAGTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1696:1688:942,746:2,1:3,1688:0.9953:2,2:39.2:1:34.8:1:1:1.58345:60:280.333:0.9959:0.02:1.1 1/1:1571:1561:918,643:2,0:2,1561:0.9936:0,2:39:1:34.9:1:0.51539:0:60:779.5:0.9949:0.021:1.1
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chr1 156785617 156785617 G A intron NTRK1 NM_001007792:c.-5G>A . . rs1800601 ID=COSV63884607;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),3(central_nervous_system) 364541 Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.636981 0.8135 0.6177 0.6667 0.4959 0.6825 0.8239 0.6358 0.6770 0.6734 0.6534 0.6243 0.5074 0.6926 0.6887 0.8288 0.6437 0.6591 0.6449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.1 1 378 1806 chr1 156785617 . G A 378 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1896;VD=1887;AF=0.9953;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45714;SOR=1.16736;LSEQ=AGGGAGTGAGTGGGCAACTC;RSEQ=GCGCATGAAGGAGGTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1896:1887:1150,737:2,1:3,1887:0.9953:2,2:41.3:1:34.8:1:1:1.28156:60:268.571:0.9968:0.0153:1.1 1/1:1806:1796:1045,751:1,0:1,1796:0.9945:0,2:41.4:1:34.8:1:1:0:60:897:0.9967:0.0244:1.1
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chr1 156830779 156830779 G A exonic NTRK1 . nonsynonymous SNV NTRK1:NM_001012331:exon1:c.53G>A:p.G18E,NTRK1:NM_002529:exon1:c.53G>A:p.G18E rs1007211 ID=COSV62325362;OCCURENCE=2(haematopoietic_and_lymphoid_tissue) 190294 Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified|not_provided MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity 0.000998403 . 0.0055 0.0043 0.0142 0.0089 0 0 0.0146 0 0.0004 0.0098 0.0028 0 0 0 0.0074 0.0161 0.0133 0.113 0.355 T 0.388 0.133 N 1 0.233 N 1.445 0.365 L -1.01 0.764 T -0.99 0.262 N -0.851 0.520 T 0.251 0.621 T . . . . . 0.442 0.270 N c -0.266 -0.286 1.000 0.747 0.598 0.340 0 2.66 0.305 0.222 0.173 0.947 0.534 0.005 0.169 0.308 0.238 10.150 0.418 . . . 1q23.1 0.5 343 2614 chr1 156830779 . G A 343 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2757;VD=1360;AF=0.4933;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.40513;SOR=0.98551;LSEQ=CTGGCACAGCTGGGCTGCGG;RSEQ=GCCGGGCAGCCTGCTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2757:1360:814,546:835,552:1387,1360:0.4933:2,2:38.2:1:33:1:0.87619:1.01465:60:29.909:0.4879:0.0102:1.2 0/1:2614:1299:821,478:837,470:1307,1299:0.4969:2,2:38:1:33.1:1:0.68388:1.03684:60:23.056:0.4905:0.0119:1.2
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chr1 156845493 156845494 GT - splicing NTRK1 NM_001007792:exon12:r.spl;NM_002529:exon12:r.spl;NM_001012331:exon11:r.spl . . rs766543019 ID=COSV100693241;OCCURENCE=3(central_nervous_system) 1281314 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.1764 0.1924 0.2147 0.3290 0.1776 0.1446 0.1937 0.1753 0.1494 0.1654 0.1701 0.1157 0.3598 0.1845 0.1095 0.1491 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.1 0.5 311 1773 chr1 156845492 . AGT A 311 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1783;VD=422;AF=0.2367;SHIFT3=34;MSI=18.000;MSILEN=2;SSF=0.00337;SOR=0.80963;LSEQ=CTGGGTCAAGGGCAGGGACG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1783:422:167,255:554,617:1171,422:0.2367:2,2:52.4:1:34.8:1:0.00622:1.37075:60:421:0.238:0.0079:0.2 0/1:1773:491:180,311:546,587:1133,491:0.2769:2,2:51.3:1:34.8:1:0.00002:1.60661:60:490:0.2781:0.0107:0.2
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chr1 156846233 156846233 G A exonic NTRK1 . synonymous SNV NTRK1:NM_001012331:exon13:c.1656G>A:p.Q552Q,NTRK1:NM_001007792:exon14:c.1566G>A:p.Q522Q,NTRK1:NM_002529:exon14:c.1674G>A:p.Q558Q rs6334 ID=COSV62323674;OCCURENCE=1(large_intestine),3(central_nervous_system),1(stomach),7(soft_tissue),1(lung) 276641 Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified|not_provided MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.212859 0.3204 0.1936 0.2207 0.1378 0.2169 0.3582 0.2096 0.2130 0.2237 0.2323 0.1995 0.1354 0.2076 0.2167 0.3626 0.2084 0.2161 0.2055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.1 0.5 365 2978 chr1 156846233 . G A 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3075;VD=1510;AF=0.4911;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4005;SOR=0.98582;LSEQ=AGTGCTCGGCAGGACTTCCA;RSEQ=CGTGAGGCTGAGCTGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3075:1510:919,591:916,642:1558,1510:0.4911:2,2:38.2:1:34.6:1:0.25361:1.09:60:376.5:0.4931:0.0156:1.1 0/1:2978:1473:849,624:900,595:1495,1473:0.4946:2,2:38.4:1:34.4:1:0.15649:1.1117:60:76.526:0.4941:0.0124:1.2
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chr1 156848995 156848995 C T exonic NTRK1 . synonymous SNV NTRK1:NM_001012331:exon14:c.1869C>T:p.A623A,NTRK1:NM_001007792:exon15:c.1779C>T:p.A593A,NTRK1:NM_002529:exon15:c.1887C>T:p.A629A rs6337 ID=COSV62325231;OCCURENCE=1(breast),3(lung),2(thyroid) 142267 Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.334065 0.0437 0.5568 0.5623 0.2017 0.5685 0.0360 0.7328 0.7281 0.6330 0.3900 0.5379 0.2079 0.5919 0.7351 0.0433 0.7278 0.7271 0.6219 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.1 0.5 362 2892 chr1 156848995 . C T 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2902;VD=1384;AF=0.4769;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31986;SOR=0.97433;LSEQ=GGTCTGGGGCAGCTGCTGGC;RSEQ=GTGGCTAGCCAGGTCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2902:1384:808,576:922,591:1513,1384:0.4769:2,2:37.1:1:34.9:1:0.17222:1.11209:60:1383:0.4794:0.0176:1.1 0/1:2892:1398:871,527:877,612:1489,1398:0.4834:2,2:37.3:1:34.7:1:0.06206:1.15:60:154.333:0.4836:0.0142:1.1
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chr1 161309335 161309335 - T intronic SDHC . . . rs746552469 ID=COSV61367886;OCCURENCE=2(biliary_tract) . . . . . . . . 0.1052 0.1136 0.1607 0.0408 . 0.1009 0.0946 0.1074 0.0075 0.0207 0.0077 0 0 0.0067 0.0007 0.0066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.3 0.5 220 735 chr1 161309335 . A AT 220 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=771;VD=77;AF=0.0999;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.28426;SOR=0.89589;LSEQ=AGGAGTTTTGAGTTATAATC;RSEQ=TTTTTTTTTTTCTCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:771:77:41,36:297,304:601,77:0.0999:2,2:47.5:1:35:0:0.547:1.17:60:154:0.1307:0:0.1 0/1:735:81:39,41:270,300:570,81:0.1102:2,2:45.2:1:34.8:1:0.90493:1.06:60:162:0.1441:0.0014:0.1
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chr1 162740327 162740327 T C intron DDR2 NM_001354983:exon12:c.1504+25T>C;NM_001354982:exon12:c.1504+25T>C;NM_006182:exon12:c.1504+25T>C;NM_001014796:exon13:c.1504+25T>C . . rs1780003 ID=COSV100906335;OCCURENCE=3(central_nervous_system) 249493 Squamous_cell_lung_carcinoma|Spondyloepimetaphyseal_dysplasia-short_limb-abnormal_calcification_syndrome|Warburg-Cinotti_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0010077,MedGen:C1849011,OMIM:271665,Orphanet:ORPHA93358|MONDO:MONDO:0032579,MedGen:C5193019,OMIM:618175|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.945487 1 0.9476 0.9853 0.8427 0.9933 0.9999 1 0.9992 0.9928 0.9995 0.9541 0.8402 0.9928 1 1 1 0.9993 0.9867 0.0 0.912 D . . . 1 0.090 P . . . 1.39 0.338 T 0.31 0.040 N -1.062 0.113 T 0.010 0.035 T . . . . . 0.019 0.059 N c -1.941 -2.171 1.000 0.747 0.487 0.133 0 -10.1 0.003 -1.387 0.026 -2.869 0.002 0.000 0.063 0.000 0.016 0.572 0.006 . . . 1q23.3 1 387 2595 chr1 162740327 . T C 387 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2553;VD=2536;AF=0.9933;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27737;SOR=1.27545;LSEQ=GGATGATGTGGTGGGCAGGG;RSEQ=GTCAAGGGAGAAACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2553:2536:1523,1013:3,3:6,2536:0.9933:2,2:37.1:1:34.1:1:0.68849:1.50:60:73.588:0.9952:0.0149:1.1 1/1:2595:2573:1534,1039:5,2:7,2573:0.9915:2,2:37.4:1:34.2:1:0.70851:1.69296:60:79.406:0.9941:0.0131:1.1
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chr1 162743418 162743418 G T intron DDR2 NM_001354983:exon14:c.1856+32G>T;NM_001354982:exon14:c.1856+32G>T;NM_006182:exon14:c.1856+32G>T;NM_001014796:exon15:c.1856+32G>T . . rs1355287 ID=COSV100906338;OCCURENCE=3(central_nervous_system) 249495 Squamous_cell_lung_carcinoma|Spondyloepimetaphyseal_dysplasia-short_limb-abnormal_calcification_syndrome|Warburg-Cinotti_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0010077,MedGen:C1849011,OMIM:271665,Orphanet:ORPHA93358|MONDO:MONDO:0032579,MedGen:C5193019,OMIM:618175|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.992412 1 0.9948 0.9985 0.9841 0.9996 1 1 1 1 0.9996 0.9958 0.9855 1 1 1 1 1 0.9980 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.3 1 370 1491 chr1 162743418 . G T 370 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1575;VD=1568;AF=0.9956;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10374;SOR=0.301;LSEQ=ACATTTTGAATTTTCCTTTA;RSEQ=GTATTTCATCTTTAGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1575:1568:663,905:0,0:0,1568:0.9956:0,2:40:1:34.9:1:1:0:60:391:0.9981:0.0489:1.1 1/1:1491:1489:618,871:0,0:0,1489:0.9987:0,2:39.9:1:35:1:1:0:60:1488:1:0.0469:1.1
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chr1 162749856 162749857 TC - splicing DDR2 NM_001354983:exon18:r.spl;NM_001354982:exon18:r.spl;NM_006182:exon18:r.spl;NM_001014796:exon19:r.spl . . rs745385978 ID=COSV100906906;OCCURENCE=1(stomach) 861295 Squamous_cell_lung_carcinoma Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782 no_assertion_criteria_provided Uncertain_significance . . 0.0063 0.0118 0.0043 0.0045 0.0037 0.0012 0.0084 0.0198 0.0414 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q23.3 0.5 254 2254 chr1 162749855 . TTC T 254 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2392;VD=155;AF=0.0648;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=0.07015;SOR=1.21081;LSEQ=TTTCCCCCGTCTTTGTAATA;RSEQ=TCTCTCTCTCTCTCTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2392:155:95,60:1357,864:2221,155:0.0648:2,2:45:1:35:1:1:1.01:60:310:0.0651:0.0071:0.2 0/1:2254:122:73,49:1206,919:2125,122:0.0541:2,2:41.8:1:34.9:1:0.51248:1.14:60:244:0.0546:0.0062:0.3
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chr1 204501383 204501383 C T intron MDM4 NM_001278516:exon5:c.343+9C>T;NM_001278518:exon5:c.343+9C>T;NM_001204171:exon5:c.343+9C>T;NM_002393:exon5:c.343+9C>T . . rs4252697 ID=COSV65797201;OCCURENCE=1(breast),8(meninges),2(haematopoietic_and_lymphoid_tissue),4(soft_tissue) . . . . . 0.198083 0.4018 0.1557 0.1881 0.0753 0.0640 0.3853 0.2105 0.1920 0.2046 0.2180 0.1771 0.0792 0.0859 0.1987 0.3660 0.2064 0.2104 0.1986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q32.1 0.5 319 1094 chr1 204501383 . C T 319 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1041;VD=516;AF=0.4957;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09029;SOR=0.88719;LSEQ=CTGCTACTACAGGTATGTCA;RSEQ=ATCATATTTCTTCAGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1041:516:228,288:232,290:522,516:0.4957:2,2:41.8:1:34.9:1:0.95022:1.01052:60:1032:0.5005:0.0086:1.1 1/0:1094:575:244,331:242,276:518,575:0.5256:2,2:40.4:1:34.8:1:0.16124:1.18925:60:574:0.5256:0.0128:1.1
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chr1 204512100 204512100 T C intron MDM4 NM_001278516:exon7:c.604+28T>C;NM_001278516:exon7:UTR3;NM_001204171:exon8:c.672+28T>C;NM_001278517:exon5:c.378+28T>C;NM_002393:exon8:c.672+28T>C . . rs4252717 ID=COSV65794912;OCCURENCE=17(soft_tissue),2(lung),1(upper_aerodigestive_tract) . . . . . 0.535144 0.7024 0.5415 0.6400 0.2732 0.6240 0.6866 0.7902 0.6901 0.6778 0.6015 0.5961 0.2859 0.5957 0.6225 0.6482 0.7934 0.7178 0.6888 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q32.1 1 347 1288 chr1 204512100 . T C 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1218;VD=1207;AF=0.991;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.44825;SOR=0.85864;LSEQ=TCACATTTGAAGGGAAGTGG;RSEQ=TTTTTTTCTTTTGAAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1218:1207:466,741:1,2:3,1207:0.991:2,2:39.6:1:32.8:1:1:1.26:60:22.667:0.9966:0.0016:1.2 1/1:1288:1278:503,775:2,1:3,1278:0.9922:2,2:38.3:1:33.7:1:0.56554:3.07876:60:38.938:0.9968:0.0256:1.2
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chr1 204513647 204513647 - T intron MDM4 NM_001278516:exon8:c.605-16->T;NM_001278516:exon8:UTR3;NM_001278517:exon6:c.379-16->T;NM_002393:exon9:c.673-16->T . . rs745539835 ID=COSV65795179;OCCURENCE=1(large_intestine) . . . . . . . . 0.0001 0.0002 0 0.0001 0 0.0001 0 0.0003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q32.1 0.25 153 1939 chr1 204513647 . G GT 153 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1927;VD=21;AF=0.0109;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.30587;SOR=1.24559;LSEQ=GAATACAGAAACTCATGTTT;RSEQ=TTTTTTTTCTGTTAGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1927:21:15,6:1100,634:1734,21:0.0109:2,2:33:1:35:1:0.50345:1.44:60:42:0.0122:0.0026:0.1 0/0:1939:17:13,4:1165,669:1834,17:0.0088:2,2:40.4:1:35:1:0.32069:1.87:60:34:0.0094:0.001:0
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chr1 204516025 204516025 A G intron MDM4 NM_001278516:exon9:c.835+20A>G;NM_001278516:exon9:UTR3;NM_001278519:exon4:c.234+20A>G;NM_001278518:exon6:c.424+20A>G;NM_001278518:exon6:UTR3;NM_001204171:exon9:c.753+20A>G;NM_001278517:exon7:c.609+20A>G;NM_002393:exon10:c.903+20A>G . . rs2290854 ID=COSV65794941;OCCURENCE=18(soft_tissue),1(lung),14(meninges),1(upper_aerodigestive_tract) . . . . . 0.539337 0.7024 0.5536 0.6433 0.2775 0.6273 0.6879 0.7914 0.6958 0.6777 0.6001 0.6003 0.2930 0.5993 0.6324 0.6473 0.7944 0.7221 0.6908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1q32.1 1 333 911 chr1 204516025 . A G 333 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=781;VD=778;AF=0.9962;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09814;SOR=0;LSEQ=GGTATGAATCTTTAGCAAGA;RSEQ=CTATTTTGCACCAGCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:781:778:323,455:0,0:0,778:0.9962:0,2:38.5:1:33.5:1:1:0:60:32.826:0.9987:0.0192:1.1 1/1:911:911:394,517:0,0:0,911:1:0,2:37.9:1:33.9:1:1:0:60:38.609:1:0.0187:1.1
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chr2 17938501 17938501 A G intronic GEN1 . . . rs2615051 . . . . . . 0.573682 0.9216 . . . . . . . . . 0.4543 0.2296 0.6724 0.5066 0.9254 0.5052 0.5054 0.5397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p24.2 1 326 819 chr2 17938501 . A G 326 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=826;VD=826;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24772;SOR=0;LSEQ=TAGGGGTTTCCAATAATCGA;RSEQ=TCAGTGCTGGACTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:826:826:468,358:0,0:0,826:1:0,2:39.9:1:33.7:1:1:0:60:42.474:1:0.0266:1.1 1/1:819:817:494,323:0,0:0,817:0.9976:0,2:38.7:1:33.8:1:1:0:60:33.042:1:0.0281:1.1
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chr2 25462327 25462327 C G intronic DNMT3A . . . rs72810046 ID=COSV53044094;OCCURENCE=3(soft_tissue) 1286041 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0866613 . . 0.0825 0.1936 0.0733 0 0.1333 0.1557 0.0508 0.0516 0.1365 0.1585 0.0728 0.1854 0 0.1563 0.1364 0.1365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.3 0.5 352 2293 chr2 25462327 . C G 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2131;VD=1058;AF=0.4965;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.28699;SOR=1.0363;LSEQ=CTGCGATGGTGGGTTGTCCT;RSEQ=TACACTGTTCAATTCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2131:1058:611,447:612,452:1064,1058:0.4965:2,2:39.5:1:34.8:1:0.93001:1.01:60:210.6:0.4988:0.0094:1.1 0/1:2293:1118:663,455:695,475:1170,1118:0.4876:2,2:39.7:1:34.8:1:0.96606:1.00413:60:278.5:0.4888:0.0214:1.1
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chr2 25469502 25469502 C T exonic DNMT3A . synonymous SNV DNMT3A:NM_001320893:exon5:c.810G>A:p.L270L,DNMT3A:NM_153759:exon6:c.699G>A:p.L233L,DNMT3A:NM_022552:exon10:c.1266G>A:p.L422L,DNMT3A:NM_175629:exon10:c.1266G>A:p.L422L rs2276598 ID=COSV53040646;OCCURENCE=1(breast),1(liver),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),2(lung),1(thyroid) 1154097 Tatton-Brown-rahman_syndrome|not_provided MONDO:MONDO:0014382,MedGen:C4014545,OMIM:615879,Orphanet:ORPHA404443|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.223842 0.3204 0.2049 0.1921 0.2970 0.2056 0.3121 0.2216 0.1729 0.1877 0.1207 0.2202 0.2884 0.2124 0.1921 0.3213 0.2285 0.1702 0.1984 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.3 0.5 338 1822 chr2 25469502 . C T 338 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1764;VD=835;AF=0.4734;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29333;SOR=0.96213;LSEQ=CATTTACCTTCTGGTGGCTC;RSEQ=AGGCCCTTAGGGCCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1764:835:548,287:632,295:927,835:0.4734:2,2:38.7:1:34.8:1:0.26469:1.12193:60:416.5:0.4741:0.0023:1.1 0/1:1822:880:576,304:628,314:942,880:0.483:2,2:37.6:1:34.6:1:0.58644:1.05549:60:175:0.4832:0.0247:1.1
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chr2 25469913 25469913 C T intron DNMT3A NM_001320893:exon4:c.666+7G>A;NM_175629:exon9:c.1122+7G>A;NM_022552:exon9:c.1122+7G>A;NM_153759:exon5:c.555+7G>A . . rs2276599 ID=COSV53038205;OCCURENCE=1(large_intestine),1(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 1154098 Tatton-Brown-rahman_syndrome|not_provided MONDO:MONDO:0014382,MedGen:C4014545,OMIM:615879,Orphanet:ORPHA404443|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.614018 0.6131 0.6863 0.7151 0.5694 0.7561 0.6053 0.8313 0.7626 0.7701 0.6103 0.7006 0.5654 0.7363 0.6656 0.6001 0.8238 0.7565 0.7525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.3 1 358 1251 chr2 25469913 . C T 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1269;VD=1269;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24634;SOR=0;LSEQ=CTCCGAGCTCCCAGCAGGGA;RSEQ=ACTCACCTGCAGGACCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1269:1269:776,493:0,0:0,1269:1:0,2:37.6:1:34.8:1:1:0:60:1268:1:0.0339:1.1 1/1:1251:1249:782,467:0,0:0,1249:0.9984:0,2:37.8:1:34.8:1:1:0:60:311.25:0.9984:0.032:1.1
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chr2 29416366 29416366 G C exonic ALK . nonsynonymous SNV ALK:NM_001353765:exon10:c.1383C>G:p.D461E,ALK:NM_004304:exon29:c.4587C>G:p.D1529E rs1881421 ID=COSV66569695;OCCURENCE=1(breast),8(meninges),1(large_intestine),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 137215 Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.572883 0.7292 0.4335 0.4672 0.6248 0.6738 0.7459 0.4837 0.3572 0.3862 0.4665 0.4808 0.6142 0.6055 0.3377 0.7553 0.4851 0.3704 0.4510 1.0 0.010 T 0.119 0.191 N 1 0.090 P -0.695 0.019 N 1.7 0.269 T 1.22 0.011 N -0.993 0.319 T 0.000 0.000 T . . . . . 0.000 0.004 N c -1.813 -1.750 0.923 0.267 0.487 0.133 0 -3.42 0.045 -0.102 0.108 -1.050 0.020 0.000 0.063 0.000 0.016 11.802 0.512 . . . 2p23.2 0.5 356 2641 chr2 29416366 . G C 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2608;VD=1286;AF=0.4931;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28908;SOR=1.03277;LSEQ=TCCAGCCCCAGGTTACCCCT;RSEQ=TCGTGTGGCTCCTTCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2608:1286:771,515:709,609:1318,1286:0.4931:2,2:37.4:1:34.5:1:0.00155:1.29:60:97.923:0.493:0.0176:1.3 0/1:2641:1281:685,596:728,626:1354,1281:0.485:2,2:39:1:34.4:1:0.90668:1.01184:60:79.062:0.4839:0.0095:1.3
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chr2 29416481 29416481 T C exonic ALK . nonsynonymous SNV ALK:NM_001353765:exon10:c.1268A>G:p.K423R,ALK:NM_004304:exon29:c.4472A>G:p.K1491R rs1881420 ID=COSV66555753;OCCURENCE=2(breast),6(meninges),3(central_nervous_system),8(soft_tissue),3(prostate),1(lung) 137213 Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.415136 0.7312 0.2234 0.3425 0.2520 0.6074 0.7469 0.2917 0.2243 0.2781 0.4324 0.2737 0.2434 0.5334 0.2067 0.7540 0.3057 0.2181 0.2882 0.408 0.102 T 0.003 0.352 U 1.000 0.266 P 1.475 0.372 L -1.1 0.773 T -0.42 0.142 N -0.933 0.438 T 0.000 0.000 T . . . . . 0.922 0.549 D c -0.425 -0.343 0.883 0.256 0.487 0.133 0 1.9 0.247 1.813 0.384 0.121 0.210 1.000 0.715 0.987 0.523 6.850 0.230 . . . 2p23.2 0.5 358 2494 chr2 29416481 . T C 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2571;VD=1291;AF=0.5021;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11343;SOR=1.07198;LSEQ=TGTTTCTGGATCCGTGGACC;RSEQ=TGTGCAACTCCGAAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2571:1291:740,551:739,538:1277,1291:0.5021:2,2:38.9:1:34.7:1:0.78001:1.02278:60:257.2:0.5018:0.0062:1.7 0/1:2494:1209:719,490:730,545:1275,1209:0.4848:2,2:37.9:1:34.6:1:0.27176:1.10:60:240.8:0.4849:0.0156:1.7
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chr2 29416572 29416572 T C exonic ALK . nonsynonymous SNV ALK:NM_001353765:exon10:c.1177A>G:p.I393V,ALK:NM_004304:exon29:c.4381A>G:p.I1461V rs1670283 ID=COSV101201052;OCCURENCE=18(meninges),3(central_nervous_system) 137211 Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.992212 1 0.9903 0.9972 0.9700 0.9990 1 1 0.9997 0.9986 1 0.9907 0.9680 0.9940 0.9934 1 1 0.9999 0.9990 1.0 0.010 T 0.683 0.061 N 1 0.090 P -1.1 0.010 N -0.89 0.748 T 0.37 0.036 N -0.987 0.333 T 0.000 0.000 T . . . . . 0.005 0.023 N c -1.265 -1.247 0.774 0.237 0.487 0.133 0 -0.134 0.128 -0.984 0.038 -1.039 0.021 0.000 0.063 0.001 0.043 8.386 0.315 . . . 2p23.2 1 389 2424 chr2 29416572 . T C 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2496;VD=2488;AF=0.9968;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38282;SOR=1.28825;LSEQ=TCTAGGGACTCGAACAGAGA;RSEQ=CTCTGCAGCTGTGGGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2496:2488:1425,1063:0,0:0,2488:0.9968:0,2:38.4:1:34.5:1:1:0:60:102.667:0.9988:0.0304:1.3 1/1:2424:2414:1400,1014:0,2:2,2414:0.9959:0,2:37.9:1:34.5:1:0.17674:0:60:159.933:0.9983:0.038:1.3
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chr2 29430943 29430944 TC - intronic ALK . . . rs3832036 ID=COSV101201649;OCCURENCE=6(meninges),3(central_nervous_system) . . . . . 0.389577 0.7163 . 0.3417 0.1809 0.2889 0.8047 . 0.1830 0.2627 0.3966 0.2598 0.1846 0.5419 0.22 0.7381 0.3207 0.2216 0.2867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 306 984 chr2 29430942 . GTC G 306 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=987;VD=444;AF=0.4498;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.31433;SOR=1.04914;LSEQ=CTGAGGACATAAATAGGTCA;RSEQ=TCTCTCTCCCAAGGATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:987:444:208,236:259,283:542,444:0.4498:2,2:43.2:1:34.8:1:0.79773:1.03837:60:221:0.451:0.0274:0.1 0/1:984:431:228,203:291,261:552,431:0.438:2,2:44.5:1:34.9:1:1:1.01:60:862:0.4398:0.0213:0.1
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chr2 29444095 29444095 C T intronic ALK . . . rs1569156 ID=COSV101201682;OCCURENCE=2(meninges),3(central_nervous_system) . . . . . 0.914736 0.9286 . 0.9806 0.7977 0.9777 0.9459 1 0.9967 0.9914 0.9860 0.9329 0.7762 0.9833 0.9934 0.9414 1 0.9995 0.9898 . . . . . . 1 0.090 P . . . . . . . . . . . . . . . . . . . . 0.003 0.016 N c -1.056 -1.234 0.729 0.230 0.554 0.246 0 -1.17 0.091 0.004 0.129 -0.839 0.030 0.000 0.063 0.003 0.074 6.727 0.224 . . . 2p23.2 1 393 2553 chr2 29444095 . C T 393 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2511;VD=2510;AF=0.9996;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11317;SOR=4.92397;LSEQ=TGAAGCAAAACAACTGCTTC;RSEQ=AAGAGAGACTGGGTGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2511:2510:1286,1224:0,0:0,2510:0.9996:0,2:38.1:1:34.6:1:1:0:60:357.571:0.9996:0.01:1.1 1/1:2553:2548:1346,1202:3,0:3,2548:0.998:0,2:36.7:1:34.8:1:0.2522:0:60:282.111:0.9984:0.0145:1.1
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chr2 29445809 29445809 T C intronic ALK . . . rs11685441 . . . . . . 0.130591 0.0119 . . . . . . . . . 0.2166 0.0494 0.1519 0.3233 0.0068 0.3335 0.3075 0.2689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 339 2004 chr2 29445809 . T C 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1943;VD=945;AF=0.4864;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.15279;SOR=1.06964;LSEQ=CGGGGGAGGTTCATGCTCCT;RSEQ=GGGGAGAGACAGATCACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1943:945:592,353:618,373:991,945:0.4864:2,2:36.6:1:34.3:1:0.92518:1.01:60:134:0.4848:0.0103:2 0/1:2004:941:582,359:691,370:1061,941:0.4696:2,2:37:1:34.5:1:0.13651:1.1519:60:133.429:0.4684:0.0075:2
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chr2 29445982 29445982 G C intronic ALK . . . rs11689436 . 1217112 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.25599 0.0546 . . . . . . . . . 0.3873 0.2100 0.2410 0.4834 0.0327 0.5147 0.5011 0.4600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 359 2723 chr2 29445982 . G C 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2701;VD=1349;AF=0.4994;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.41452;SOR=1.01329;LSEQ=ATCTGAATGAATTTTGAGGA;RSEQ=AGCCCTGGTTCTCCTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2701:1349:835,514:841,508:1349,1349:0.4994:2,2:39:1:34.5:1:0.84271:1.01908:60:121.636:0.5002:0:1.1 0/1:2723:1351:854,497:883,484:1367,1351:0.4961:2,2:38.1:1:34.6:1:0.47223:1.06168:60:224.167:0.4983:0.0066:1.1
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chr2 29446202 29446202 G A intron ALK NM_001353765:exon1:c.155+6C>T;NM_004304:exon20:c.3359+6C>T . . rs4622670 ID=COSV66569119;OCCURENCE=1(breast),7(meninges),1(lung) 250717 Neuroblastoma_3|not_specified|not_provided MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.176518 0.0536 0.2663 0.2862 0.0557 0.1579 0.0339 0.3568 0.3575 0.3594 0.3549 0.2520 0.0629 0.1818 0.3543 0.0327 0.3506 0.3609 0.3092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 366 3016 chr2 29446202 . G A 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3079;VD=1542;AF=0.5008;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25495;SOR=1.03572;LSEQ=TCCCAGGACGGCAGCAGGGC;RSEQ=CTCACCGAATGAGGGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3079:1542:887,655:887,641:1528,1542:0.5008:2,2:38.4:1:34.6:1:0.77016:1.02184:60:139.182:0.5028:0.0169:1.1 0/1:3016:1484:886,598:909,616:1525,1484:0.492:2,2:38.2:1:34.6:1:0.97036:1.00:60:163.889:0.4936:0.0196:1.1
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chr2 29446701 29446701 T C intron ALK NM_001353765:c.-339A>G . . rs12619049 ID=COSV66558292;OCCURENCE=15(soft_tissue) 1261836 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.305711 0.1587 . . . . . . . . . 0.3932 0.4174 0.2649 0.4205 0.1656 0.3302 0.4251 0.3939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 345 2103 chr2 29446701 . T C 345 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2112;VD=1014;AF=0.4801;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43469;SOR=0.98803;LSEQ=AGATGGGATTAGACCCAATA;RSEQ=GGTCTGCAGATTTTATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2112:1014:630,384:690,406:1096,1014:0.4801:2,2:38.3:1:34.4:1:0.71878:1.03589:60:111.667:0.4788:0.009:2 0/1:2103:1016:642,374:696,390:1086,1016:0.4831:2,2:38.9:1:34.6:1:0.68313:1.03964:60:337.667:0.4828:0.0114:2
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chr2 29446721 29446721 A G intron ALK NM_001353765:c.-359T>C . . rs4665447 ID=COSV101201686;OCCURENCE=3(central_nervous_system) . . . . . 0.854633 0.9187 . . . . . . . . . 0.8794 0.6369 0.9617 0.9669 0.9340 0.9759 0.9801 0.9622 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 1 379 2209 chr2 29446721 . A G 379 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2241;VD=2233;AF=0.9964;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29936;SOR=0.63329;LSEQ=TGGTCTGCAGATTTTATTAG;RSEQ=AGAAATGCCCATGAGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2241:2233:1409,824:0,0:0,2233:0.9964:0,2:37.3:1:34.1:1:1:0:60:66.667:0.9991:0.0593:1.5 1/1:2209:2204:1442,762:0,1:1,2204:0.9977:0,2:37.9:1:34.1:1:0.34603:0:60:54.1:0.9991:0.0611:1.5
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chr2 29447108 29447108 G A intronic ALK . . . rs4387740 ID=COSV101201687;OCCURENCE=3(central_nervous_system) . . . . . 0.727436 0.755 . . . . . . . . . 0.7086 0.6098 0.7947 0.7152 0.7670 0.8268 0.7242 0.7495 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 363 2906 chr2 29447108 . G A 363 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2742;VD=1346;AF=0.4909;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10031;SOR=1.07208;LSEQ=CACATCATGAAAAGATCTCT;RSEQ=AATTGGTGTCTGGGGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2742:1346:781,565:789,606:1395,1346:0.4909:2,2:39.5:1:34.9:1:0.4402:1.06:60:447.667:0.4921:0.0051:1.1 0/1:2906:1376:761,615:852,678:1530,1376:0.4735:2,2:39.5:1:34.9:1:0.85177:1.01555:60:1375:0.4743:0.0048:1.1
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chr2 29447253 29447253 A G intronic ALK . . . rs6723311 ID=COSV101201688;OCCURENCE=3(central_nervous_system) . . . . . 0.629393 0.8581 . . . . . . . . . 0.5322 0.4892 0.7375 0.5364 0.8872 0.5295 0.5070 0.5439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 349 2777 chr2 29447253 . A G 349 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2709;VD=1360;AF=0.502;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34333;SOR=1.02352;LSEQ=CCTGCCCTGTTTCCCTAACC;RSEQ=CTGCCACTCCCCACCCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2709:1360:732,628:734,610:1344,1360:0.502:2,2:36.9:1:33:1:0.69953:1.03232:60:20.587:0.4911:0.0218:1.1 0/1:2777:1378:727,651:728,660:1388,1378:0.4962:2,2:36.4:1:33.5:1:0.87899:1.01:60:39.529:0.4912:0.0284:1.1
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chr2 29448760 29448760 C T intronic ALK . . . rs34935102 ID=COSV66558297;OCCURENCE=11(soft_tissue) 1269165 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.177915 0.121 . . . . . . . . . 0.2081 0.2094 0.1691 0.2384 0.1400 0.1163 0.2386 0.1939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 360 2632 chr2 29448760 . C T 360 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2708;VD=1365;AF=0.5041;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45224;SOR=0.99196;LSEQ=TCTGGAAGAGATGTGGGGGC;RSEQ=GCAGGTGACCAAACAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2708:1365:839,526:798,530:1328,1365:0.5041:2,2:36.5:1:34.6:1:0.47747:1.06:60:272:0.5082:0.0281:1.1 1/0:2632:1332:833,499:777,505:1282,1332:0.5061:2,2:36.8:1:34.4:1:0.31489:1.08:60:82.25:0.5093:0.0198:1.1
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chr2 29448846 29448846 C G intronic ALK . . . rs11683248 . . . . . . 0.256789 0.0546 . . . . . . . . . 0.3521 0.3117 0.1814 0.3907 0.0358 0.4512 0.3948 0.3650 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 358 2662 chr2 29448846 . C G 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2773;VD=1311;AF=0.4728;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21482;SOR=0.95657;LSEQ=GCCCTGAGGCACTGGGCTCA;RSEQ=AGTGGGGAGGGGTCCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2773:1311:706,605:807,646:1453,1311:0.4728:2,2:36.1:1:34.6:1:0.379:1.07049:60:144.667:0.474:0.0245:1.1 0/1:2662:1288:747,541:802,569:1371,1288:0.4838:2,2:37.5:1:34.6:1:0.8134:1.02079:60:160:0.4845:0.0222:1.1
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chr2 29449423 29449423 G A intronic ALK . . . rs6744522 . . . . . . 0.305112 0.0516 . . . . . . . . . 0.4403 0.2829 0.3270 0.4597 0.0315 0.5762 0.5481 0.4856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 1 362 1358 chr2 29449423 . G A 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1385;VD=1379;AF=0.9957;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2897;SOR=1.53311;LSEQ=GCACATGCACAGCTGCTGCT;RSEQ=TAAGGAAACCTAGGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1385:1379:911,468:0,0:0,1379:0.9957:0,2:35.2:1:34.8:1:1:0:60:274.8:0.9978:0.0679:1.1 1/1:1358:1349:883,466:0,0:0,1349:0.9934:0,2:35:1:34.6:1:1:0:60:148.889:0.9985:0.0508:1.1
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chr2 29455199 29455199 A T exonic ALK . nonsynonymous SNV ALK:NM_004304:exon15:c.2603T>A:p.L868Q rs55941323 . 289379 Neuroblastoma_3 MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014 criteria_provided,_multiple_submitters,_no_conflicts Uncertain_significance 0.000199681 . . 1.883e-05 0 0 0 0 3.68e-05 0 0 3.23e-05 0 0 0 0 0 6.669e-05 0 0.303 0.143 T 0.062 0.221 N 0.952 0.810 D 1.1 0.281 L -1.08 0.771 T 0.33 0.039 N -0.902 0.478 T 0.180 0.528 T 0.096 0.766 D 0.062 0.002 0.854 0.442 D c -0.308 -0.128 0.009 0.119 0.500 0.196 0 4.27 0.498 4.268 0.584 0.202 0.252 1.000 0.715 0.046 0.161 4.448 0.109 . . . 2p23.2 0.5 360 2616 chr2 29455199 . A T 360 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2538;VD=1280;AF=0.5043;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08365;SOR=1.08167;LSEQ=CGGAATTGCCGTTTAGCCCT;RSEQ=GAACCGAGGAGTTATTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2538:1280:788,492:786,465:1251,1280:0.5043:2,2:38.9:1:34.9:1:0.51223:1.05533:60:2560:0.5065:0.0213:1.8 0/1:2616:1268:799,469:834,511:1345,1268:0.4847:2,2:38:1:34.9:1:0.59946:1.04:60:421.667:0.4849:0.0191:1.8
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chr2 29455267 29455267 A G exonic ALK . synonymous SNV ALK:NM_004304:exon15:c.2535T>C:p.G845G rs2256740 ID=COSV66555763;OCCURENCE=1(breast),1(liver),16(meninges),1(bone),1(haematopoietic_and_lymphoid_tissue),1(stomach),19(soft_tissue) 250719 Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.5 0.1746 0.6614 0.6048 0.5410 0.4341 0.1763 0.6628 0.7102 0.6960 0.5852 0.6208 0.5538 0.4880 0.7583 0.1811 0.6663 0.7009 0.6288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 1 388 2765 chr2 29455267 . A G 388 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2586;VD=2568;AF=0.993;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06775;SOR=1.6175;LSEQ=TTGGCCCCGTAGGCCCTGCC;RSEQ=CCACCTCCGGCTGCAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2586:2568:1454,1114:1,4:5,2568:0.993:2,2:37.4:1:33.8:1:0.1737:5.22:60:39.762:0.996:0.0263:1.4 1/1:2765:2734:1495,1239:1,5:6,2734:0.9888:2,2:37:1:34:1:0.0981:6.03:60:50.585:0.9944:0.0539:1.4
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chr2 29497967 29497967 G A exonic ALK . nonsynonymous SNV ALK:NM_004304:exon11:c.2039C>T:p.T680I rs35228363 ID=COSV66555766;OCCURENCE=1(ovary),2(soft_tissue) 137201 Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.00998403 0.001 0.0210 0.0154 0.0047 0.0109 0 0.0172 0.0234 0.0216 0.0040 0.0164 0.0053 0.0203 0.0033 0 0.0203 0.0238 0.0173 0.113 0.287 T 0.051 0.230 U 1.000 0.810 D 2.075 0.572 M -1.16 0.781 T -1.22 0.309 N -0.717 0.596 T 0.157 0.490 T . . . . . 0.897 0.500 D c 0.022 0.148 1.000 0.747 0.516 0.203 0 5.21 0.719 4.562 0.603 0.953 0.551 1.000 0.715 0.995 0.604 14.292 0.657 . . . 2p23.2 0.5 348 2131 chr2 29497967 . G A 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2034;VD=1035;AF=0.5088;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00213;SOR=1.19625;LSEQ=TGTGAGCTGAACCCTTACCT;RSEQ=TAGGGTCAAAGATGGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2034:1035:634,401:597,402:999,1035:0.5088:2,2:40:1:34.8:1:0.49645:1.06:60:344:0.5094:0.0128:1.1 0/1:2131:989:620,369:712,428:1140,989:0.4641:2,2:38.4:1:34.9:1:0.92848:1.01:60:988:0.4649:0.0164:1.1
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chr2 29543663 29543663 T C exonic ALK . synonymous SNV ALK:NM_004304:exon7:c.1500A>G:p.Q500Q rs2293564 ID=COSV66566490;OCCURENCE=18(meninges),3(central_nervous_system),1(thyroid) 250720 Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.776558 0.9206 0.7909 0.8702 0.5078 0.8881 0.9077 0.9187 0.9174 0.9193 0.8626 0.8023 0.5071 0.8771 0.8808 0.9086 0.9241 0.9216 0.8939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 1 386 2344 chr2 29543663 . T C 386 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2402;VD=2388;AF=0.9942;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52562;SOR=0.95127;LSEQ=TTTAGGGTCCTGACCTGCCA;RSEQ=TGAGGAGTGTGGGGTGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2402:2388:1472,916:1,0:1,2388:0.9942:0,2:39.7:1:34.4:1:1:0:60:87.444:0.9966:0.0204:1.1 1/1:2344:2331:1417,914:1,0:1,2331:0.9945:0,2:38.3:1:34.3:1:1:0:60:136.118:0.9961:0.0124:1.1
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chr2 29551161 29551161 G A intronic ALK . . . rs62130643 ID=COSV66571291;OCCURENCE=1(lung) 1228708 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.124601 0.0099 . . . . . . . . . 0.1755 0.0768 0.1062 0.2351 0.0025 0.1872 0.2498 0.2077 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 0.5 335 1556 chr2 29551161 . G A 335 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1526;VD=740;AF=0.4849;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24393;SOR=0.9488;LSEQ=CCTGGGATAATGGGGACAAC;RSEQ=GGGTTATGAGCATGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1526:740:542,198:556,227:783,740:0.4849:2,2:36.1:1:34.9:1:0.3605:1.12:60:1480:0.4862:0.0229:1.1 0/1:1556:775:576,199:564,215:779,775:0.4981:2,2:36.2:1:35:1:0.4218:1.10:60:1550:0.4997:0.0129:1.1
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chr2 29940529 29940529 A T exonic ALK . synonymous SNV ALK:NM_004304:exon2:c.702T>A:p.P234P rs2246745 ID=COSV66584548;OCCURENCE=17(meninges),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 250722 Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.589257 0.7827 0.6270 0.7284 0.2392 0.7226 0.7582 0.7449 0.8084 0.7723 0.7152 0.6361 0.2397 0.7224 0.7881 0.7342 0.7362 0.8163 0.7633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.2 1 381 2076 chr2 29940529 . A T 381 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2087;VD=2083;AF=0.9981;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03726;SOR=3.02704;LSEQ=AAATAATCAGGAGAAGGAGA;RSEQ=GGCATGTTTGTTGGTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2087:2083:1101,982:0,0:0,2083:0.9981:0,2:39.3:1:34.6:1:1:0:60:129.188:0.9986:0.0383:1.1 1/1:2076:2064:1153,911:0,0:0,2064:0.9942:0,2:39.1:1:34.7:1:1:0:60:228.333:0.9961:0.0332:1.1
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chr2 30143499 30143499 G C exonic ALK . synonymous SNV ALK:NM_004304:exon1:c.27C>G:p.L9L rs4358080 ID=COSV66573286;OCCURENCE=4(large_intestine),3(central_nervous_system) 250724 Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.89377 0.998 0.9093 0.8944 0.8378 0.9540 1 0.8906 0.9019 0.9091 0.8765 0.8892 0.8349 0.9459 0.8245 1 0.8627 0.9123 0.9002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p23.1 1 374 2494 chr2 30143499 . G C 374 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2518;VD=2498;AF=0.9921;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36788;SOR=1.16253;LSEQ=GTGGAAAGCAGCAGCGGCAG;RSEQ=AGCCACAGGAGCCCGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2518:2498:1156,1342:3,0:3,2498:0.9921:0,2:41.1:1:33.2:1:0.09938:0:60:25.021:0.9967:0.0163:1.2 1/1:2494:2471:1145,1326:2,1:3,2471:0.9908:2,2:39.6:1:33.3:1:0.59966:2.3154:60:25.859:0.9954:0.0377:1.2
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chr2 38298150 38298150 A G exonic CYP1B1 . synonymous SNV CYP1B1:NM_000104:exon3:c.1347T>C:p.D449D rs1056837 ID=COSV52226737;OCCURENCE=2(large_intestine) 177657 Irido-corneo-trabecular_dysgenesis|Glaucoma_3,_primary_congenital,_A|Anterior_segment_dysgenesis_6|Congenital_glaucoma|not_specified|not_provided Human_Phenotype_Ontology:HP:0000659,MONDO:MONDO:0011414,MedGen:C0344559,OMIM:604229,Orphanet:ORPHA708,SNOMED_CT:204153003|MONDO:MONDO:0009277,MedGen:C1856439,OMIM:231300|MONDO:MONDO:0015016,MedGen:C4310623,OMIM:617315|MONDO:MONDO:0020366,MedGen:C0020302,Orphanet:ORPHA98976,SNOMED_CT:204113001|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.620208 0.9087 0.4537 0.6303 0.2475 0.8074 0.8989 0.6362 0.5686 0.6571 0.7929 0.5083 0.2469 0.7584 0.4834 0.8905 0.6354 0.5701 0.5959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p22.2 0.5 350 2421 chr2 38298150 . A G 350 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2395;VD=1150;AF=0.4802;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23231;SOR=1.04487;LSEQ=AGGTCCTTGTTGATGAGGCC;RSEQ=TCCTTGTCCAAGAATCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2395:1150:729,421:731,508:1239,1150:0.4802:2,2:39.4:1:34.5:1:0.029:1.20:60:126.778:0.4796:0.0038:1.8 0/1:2421:1136:695,441:795,486:1281,1136:0.4692:2,2:38.3:1:34.6:1:0.67521:1.03797:60:161.286:0.4687:0.0223:1.8
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chr2 38298203 38298203 C G exonic CYP1B1 . nonsynonymous SNV CYP1B1:NM_000104:exon3:c.1294G>C:p.V432L rs1056836 ID=COSV52230252;OCCURENCE=1(large_intestine) 177658 Glaucoma_3,_primary_congenital,_A|Anterior_segment_dysgenesis_6|Congenital_glaucoma|not_specified|not_provided MONDO:MONDO:0009277,MedGen:C1856439,OMIM:231300|MONDO:MONDO:0015016,MedGen:C4310623,OMIM:617315|MONDO:MONDO:0020366,MedGen:C0020302,Orphanet:ORPHA98976,SNOMED_CT:204113001|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.614816 0.9087 0.4456 0.6277 0.2246 0.8066 0.8968 0.6355 0.5680 0.6571 0.7924 0.5025 0.2253 0.7590 0.4834 0.8888 0.6355 0.5710 0.5937 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p22.2 0.5 356 2601 chr2 38298203 . C G 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2630;VD=1281;AF=0.4871;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21894;SOR=1.04549;LSEQ=CTCCGGGTTAGGCCACTTCA;RSEQ=TGGGTCATGATTCACAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2630:1281:751,530:799,541:1340,1281:0.4871:2,2:39.1:1:34.5:1:0.60561:1.04229:60:97.538:0.4868:0.0183:1.7 0/1:2601:1238:730,508:820,541:1361,1238:0.476:2,2:38.2:1:34.7:1:0.52196:1.05472:60:246.6:0.4768:0.0146:1.7
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chr2 47596853 47596853 - G intronic EPCAM . . . rs144077629 . 1214638 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.137979 0.254 . 0.0939 0.1087 0.0765 0.2647 0.1 0.0639 0.0593 0.1014 0.0960 0.1041 0.1328 0.0629 0.2385 0.1020 0.0735 0.0896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p21 0.5 350 2512 chr2 47596853 . C CG 350 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=2628;VD=1190;AF=0.4528;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03243;SOR=0.90047;LSEQ=TTTCCAGCGTGGAGACCGGA;RSEQ=GGTGCGGCCGTGCTCCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2628:1190:781,409:890,536:1426,1190:0.4528:2,2:43.3:1:34.4:1:0.09381:1.15:60:98.167:0.8408:0.0186:0.2 0/1:2512:1203:768,435:869,431:1300,1203:0.4789:2,2:40.3:1:34.3:1:0.11977:1.14195:60:119.3:0.9328:0.0561:0.2
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chr2 47601106 47601106 T C exonic EPCAM . nonsynonymous SNV EPCAM:NM_002354:exon3:c.344T>C:p.M115T rs1126497 ID=COSV55392922;OCCURENCE=1(urinary_tract),2(prostate) 181861 Lynch_syndrome_I|Diarrhea_5,_with_tufting_enteropathy,_congenital|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0013184,MedGen:C2750737,OMIM:613217,Orphanet:ORPHA92050|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.666134 0.8323 0.5667 0.5231 0.8374 0.4622 0.8275 0.6097 0.4394 0.4957 0.4885 0.6033 0.8316 0.4557 0.3775 0.8403 0.6001 0.4616 0.5545 1.0 0.010 T 0.060 0.222 N 1 0.090 P -1.4 0.006 N 0.05 0.619 T 2.21 0.003 N -0.934 0.436 T 0.000 0.000 T . . . . . 0.076 0.135 N c -1.157 -0.973 1.000 0.747 0.778 0.996 0 1.71 0.233 0.050 0.139 -0.318 0.077 0.559 0.272 0.815 0.341 11.894 0.517 Thyroglobulin type-1 ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8 Adipose_Subcutaneous|Adipose_Visceral_Omentum|Artery_Tibial|Cells_Transformed_fibroblasts|Lung|Nerve_Tibial 2p21 0.5 356 2563 chr2 47601106 . T C 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2581;VD=1296;AF=0.5021;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1146;SOR=1.07102;LSEQ=GCAGTGCAACGGCACCTCCA;RSEQ=GTGCTGGTGTGTGAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2581:1296:724,572:734,542:1276,1296:0.5021:2,2:37.8:1:34.5:1:0.4035:1.06989:60:143:0.501:0.0174:1.1 0/1:2563:1243:712,531:754,564:1318,1243:0.485:2,2:38.1:1:34.7:1:1:1.00:60:309.75:0.4847:0.016:1.1
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chr2 47635524 47635524 T - intron MSH2 NM_001258281:exon3:c.14-16T>-;NM_000251:exon2:c.212-16T>- . . rs786201069 ID=COSV51877400;OCCURENCE=1(biliary_tract),1(haematopoietic_and_lymphoid_tissue) 181902 Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . 0.0578 0.1503 0.1035 0.1847 0.1152 0.0411 0.1541 0.1446 0.1982 0.0066 0.0036 0.0238 0.0086 0.0013 0.0492 0.0040 0.0105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p21 0.5 271 1270 chr2 47635523 . CT C 271 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1261;VD=220;AF=0.1745;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.03966;SOR=1.2162;LSEQ=TATCTCAAATCTGTAATGTA;RSEQ=TTTTTTTTTTTTAAGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1261:220:131,89:623,353:976,220:0.1745:2,2:42.2:1:34.9:1:0.2465:1.19884:60:440:0.1746:0.0119:0.1 0/1:1270:188:106,82:645,367:1012,188:0.148:2,2:40.8:1:34.8:1:0.05931:1.35917:60:376:0.1485:0.0094:0.2
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chr2 47708960 47708960 T A intronic MSH2 . . . rs964696604 . . . . . . . . . . . . . . . . . 0.0010 0.0028 0.0013 0 0.0006 0 0.0002 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p21 0.25 125 1107 chr2 47708960 . T A 125 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=SNV;DP=1051;VD=8;AF=0.0076;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28964;SOR=0.70002;LSEQ=CTTTTTTTTTTTTTTTTTTT;RSEQ=AAATTAGAGGATTACTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1051:8:5,3:671,370:1041,8:0.0076:2,2:40.4:1:30.6:1:1:1.08802:60:7:0.0067:0:1 0/1:1107:12:8,4:723,369:1092,12:0.0108:2,2:42.1:1:35:0:1:1.02:60:24:0.0109:0:1.2
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chr2 48010488 48010488 G A exonic MSH6 . nonsynonymous SNV MSH6:NM_000179:exon1:c.116G>A:p.G39E,MSH6:NM_001281492:exon1:c.116G>A:p.G39E rs1042821 ID=COSV52274018;OCCURENCE=3(meninges),4(large_intestine),8(lung) 45243 Breast_carcinoma|Carcinoma_of_colon|Lynch_syndrome|Lynch_syndrome_I|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.200879 0.2758 0.1796 0.2140 0.2711 0.1111 0.2892 0.1463 0.2212 0.2148 0.2257 0.1903 0.2229 0.1214 0.2583 0.2398 0.1368 0.1813 0.1861 0.212 0.284 T 0.902 0.086 N 1.000 0.232 P 0.695 0.181 N -1.77 0.862 D -0.28 0.116 N -1.097 0.044 T 0.000 0.000 T . . . . . 0.049 0.105 N c -0.592 -0.509 1.000 0.747 0.442 0.072 0 2.63 0.303 1.784 0.381 0.787 0.318 0.984 0.356 0.250 0.228 3.328 0.066 . ENSG00000116062.10 Adipose_Subcutaneous 2p16.3 0.5 351 2929 chr2 48010488 . G A 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3083;VD=1493;AF=0.4843;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.42184;SOR=1.01158;LSEQ=CCGTGCCGCCGCTGCCCCCG;RSEQ=GGCCTCTCCTTCCCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3083:1493:888,605:935,651:1586,1493:0.4843:2,2:38.1:1:33.3:1:0.76928:1.02:60:33.721:0.4816:0.0156:1.2 0/1:2929:1410:865,545:872,643:1515,1410:0.4814:2,2:37.9:1:33.2:1:0.0383:1.17:60:29.652:0.4768:0.0143:1.2
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chr2 48028500 48028500 G TTTT intronic MSH6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.5 74 427 chr2 48028500 . G TTTT 74 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Complex;DP=366;VD=6;AF=0.0164;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.50589;SOR=1.16921;LSEQ=AGCCCTTTGGCCTTTCTTCA;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:6:0,6:196,161:357,6:0.0164:2,0:42.8:1:30.6:1:0.00903:0:60:12:0.0186:0:1 0/1:427:6:0,6:205,208:413,6:0.0141:2,0:51.5:1:29:0:0.03035:0:60:12:0.0154:0:1.3
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chr2 48029796 48029796 T A intronic MSH6 . . . rs942076368 . . . . . . . . . . . . . . . . . 0.0002 0.0005 0 0 0 0 7.051e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.25 137 922 chr2 48029796 . T A 137 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=SNV;DP=1005;VD=5;AF=0.005;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00762;SOR=0.28329;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AAATAATGGTAGTTTACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:5:1,4:650,348:998,5:0.005:2,2:45.8:1:32.8:1:0.05411:7.45645:60:10:0.005:0:1.2 0/1:922:16:9,7:570,335:905,16:0.0174:2,2:38.2:1:34.3:1:0.60768:1.32294:60:32:0.0174:0:1
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chr2 48030640 48030640 C - exonic MSH6 . frameshift deletion MSH6:NM_001281492:exon3:c.2864delC:p.F958Sfs*2,MSH6:NM_001281493:exon4:c.2348delC:p.F786Sfs*2,MSH6:NM_000179:exon5:c.3254delC:p.F1088Sfs*2,MSH6:NM_001281494:exon5:c.2348delC:p.F786Sfs*2 rs267608078 ID=COSV52273658;OCCURENCE=36(large_intestine),3(haematopoietic_and_lymphoid_tissue),11(stomach),1(thyroid),6(small_intestine),13(endometrium) 94837 Lynch-like_syndrome|Endometrial_carcinoma|Carcinoma_of_colon|Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|Mismatch_repair_cancer_syndrome_3|Hereditary_nonpolyposis_colorectal_neoplasms|not_provided .|Human_Phenotype_Ontology:HP:0012114,MONDO:MONDO:0002447,MedGen:C0476089,OMIM:608089,SNOMED_CT:254878006|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0030841,MedGen:C5436807,OMIM:619097|MedGen:C0009405|MedGen:CN517202 reviewed_by_expert_panel Pathogenic . . . 0.0002 0.0003 9.007e-05 0.0003 0 0.0001 0.0014 0.0002 3.256e-05 0 0 0 0 0.0003 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.5 171 2737 chr2 48030639 . AC A 171 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2775;VD=30;AF=0.0108;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.52132;SOR=1.02054;LSEQ=TAATTCTGTTGCCGGAAGAT;RSEQ=CCCCCCCTTCTTAGAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2775:30:15,15:1617,1126:2743,30:0.0108:2,2:35:1:35:1:0.35369:1.43584:60:60:0.0109:0.0007:0.5 0/1:2737:29:15,14:1583,1120:2703,29:0.0106:2,2:46.6:1:35:0:0.45605:1.31901:60:58:0.0107:0:0.5
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chr2 48030692 48030692 T A exonic MSH6 . synonymous SNV MSH6:NM_001281492:exon3:c.2916T>A:p.T972T,MSH6:NM_001281493:exon4:c.2400T>A:p.T800T,MSH6:NM_000179:exon5:c.3306T>A:p.T1102T,MSH6:NM_001281494:exon5:c.2400T>A:p.T800T rs2020910 ID=COSV52275019;OCCURENCE=1(soft_tissue) 45251 Carcinoma_of_colon|Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.0493211 0.2153 0.0045 0.0212 0.0085 0.0160 0.2091 0.0122 0.0023 0.0144 0.0087 0.0149 0.0073 0.0143 0 0.1813 0.0155 0.0017 0.0133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.5 363 2823 chr2 48030692 . T A 363 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2645;VD=1281;AF=0.4843;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.15508;SOR=0.94519;LSEQ=CATCCTTGCATTACGAAGAC;RSEQ=TTTTTTGGAGATGATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2645:1281:737,544:754,605:1359,1281:0.4843:2,2:38.2:1:34.8:1:0.28931:1.09:60:212.5:0.4835:0.0076:1.1 0/1:2823:1407:820,587:805,600:1405,1407:0.4984:2,2:38.2:1:34.8:1:0.61965:1.04:60:468:0.4986:0.0205:1.1
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chr2 48030838 48030838 A T intron MSH6 NM_001281492:exon3:c.3048+14A>T;NM_000179:exon5:c.3438+14A>T;NM_001281493:exon4:c.2532+14A>T;NM_001281494:exon5:c.2532+14A>T . . rs2020911 ID=COSV52273834;OCCURENCE=23(large_intestine),1(lung) 51641 Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|Breast_and/or_ovarian_cancer|not_provided MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN221562|MedGen:CN517202 reviewed_by_expert_panel Benign 0.400958 0.619 0.3146 0.4090 0.1784 0.5272 0.6209 0.3379 0.3788 0.3876 0.4788 0.3215 0.1746 0.4761 0.37 0.6412 0.3298 0.3606 0.3313 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.5 342 1725 chr2 48030838 . A T 342 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1719;VD=858;AF=0.4991;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17911;SOR=0.93713;LSEQ=GAGACAGGTAACTGATTCTT;RSEQ=AAGTTTTGTTATCAGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1719:858:386,472:405,455:860,858:0.4991:2,2:39.8:1:34.9:1:0.38408:1.08837:60:1716:0.5006:0.0268:1.1 1/0:1725:889:407,482:409,425:834,889:0.5154:2,2:39.1:1:35:1:0.17692:1.1396:60:1778:0.5154:0.0249:1.1
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chr2 48032741 48032741 T - intron MSH6 NM_001281492:exon5:c.3167-16T>-;NM_000179:exon7:c.3557-16T>-;NM_001281493:exon6:c.2651-16T>-;NM_001281494:exon7:c.2651-16T>- . . rs267608102 ID=COSV52289562;OCCURENCE=1(liver) 94891 Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . 0.0869 0.1405 0.2323 0.1908 0.1632 0.0497 0.1213 0.1444 0.1494 0.0373 0.1051 0.0255 0 0.0044 0.0337 0.0032 0.0212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.5 264 1325 chr2 48032740 . AT A 264 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1342;VD=196;AF=0.1461;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.20753;SOR=1.10204;LSEQ=AAAATGAGTATTCATTTGTG;RSEQ=TTTTTTTTTTTTAAGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1342:196:140,56:761,352:1113,196:0.1461:2,2:43.7:1:34.8:1:0.45169:1.16:60:195:0.1461:0.0075:0.1 0/1:1325:178:123,55:763,356:1119,178:0.1343:2,2:40.6:1:35:1:0.86244:1.04:60:356:0.1344:0.0106:0.1
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chr2 48033891 48033891 T - intron MSH6 NM_001281492:exon8:c.3612-27T>-;NM_000179:exon10:c.4002-27T>-;NM_001281493:exon9:c.3096-27T>-;NM_001281494:exon10:c.3096-27T>- . . rs267608137 . 94982 Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_5|not_specified|not_provided MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Likely_benign . . . 0.4238 0.3836 0.4140 0.4141 0.4351 0.4263 0.4427 0.4362 0.2881 0.3025 0.2269 0.2969 0.2251 0.3450 0.2826 0.2765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.3 0.5 293 1104 chr2 48033890 . CT C 293 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1145;VD=331;AF=0.2891;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.21393;SOR=0.92552;LSEQ=ACTATGAAAAAACAAAAAAA;RSEQ=TTTTTTTTTTTTTTTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1145:331:191,140:339,230:569,331:0.2891:2,2:42.6:1:34.8:1:0.62296:1.08026:60:662:0.2904:0.0227:0.1 0/1:1104:337:196,141:309,225:534,337:0.3053:2,2:42.9:1:34.9:1:0.94392:1.01:60:674:0.3069:0.0254:0.1
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chr2 58388696 58388696 A G exonic FANCL . synonymous SNV FANCL:NM_001114636:exon12:c.996T>C:p.S332S,FANCL:NM_018062:exon12:c.981T>C:p.S327S rs848291 ID=COSV52073421;OCCURENCE=1(stomach),2(haematopoietic_and_lymphoid_tissue) 250750 Fanconi_anemia,_complementation_group_L|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0013566,MedGen:C3469528,OMIM:614083|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.70647 0.5883 0.7041 0.6507 0.9100 0.6829 0.5596 0.6542 0.6098 0.6662 0.6627 0.6976 0.8947 0.6751 0.5430 0.5789 0.6272 0.6195 0.6442 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.1 0.5 340 1982 chr2 58388696 . A G 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1897;VD=1007;AF=0.5308;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=1.21424;LSEQ=TGGAAAGGTTGTCCACACTG;RSEQ=GAATTATCACACACTTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1897:1007:609,398:520,368:888,1007:0.5308:2,2:38.2:1:34.1:1:0.39894:1.08:60:70.929:0.5285:0.019:1.1 0/1:1982:956:546,410:606,416:1022,956:0.4823:2,2:39.5:1:33.9:1:0.33817:1.09383:60:46.8:0.479:0.0172:1.1
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chr2 58390219 58390219 A - intron FANCL NM_001114636:exon10:c.791-10T>-;NM_018062:exon10:c.776-10T>- . . rs374236117 . 1154183 Fanconi_anemia MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002 criteria_provided,_single_submitter Benign . . 0.0424 0.0926 0.0492 0.0890 0.0621 0.0145 0.0876 0.1103 0.1875 0.0022 0.0030 0 0 0 0.0135 0.0007 0.0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.1 0.5 237 1092 chr2 58390218 . TA T 237 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1031;VD=111;AF=0.1077;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.13723;SOR=1.18373;LSEQ=GGGGTTTTACCACTTCAGAT;RSEQ=AAAAAAAAAAATTTAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1031:111:43,68:370,537:907,111:0.1077:2,2:44.4:1:35:1:0.75883:1.08954:60:222:0.1078:0.0097:0.2 0/1:1092:101:47,54:372,608:980,101:0.0925:2,2:45:1:34.9:1:0.10736:1.42:60:202:0.0925:0.0055:0.2
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chr2 58390231 58390231 T A intron FANCL NM_001114636:exon10:c.791-22A>T;NM_018062:exon10:c.776-22A>T . . rs557652860 . . . . . . 0.00938498 0.0089 . 0.0011 0.0025 0.0003 0.0066 0.0042 7.893e-05 0.0044 0.0006 0.0018 0.0030 0 0 0.0099 0.0026 0.0002 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.1 0.25 121 984 chr2 58390231 . T A 121 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=927;VD=11;AF=0.0119;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04611;SOR=2.9406;LSEQ=TTCAGATTAAAAAAAAAAAA;RSEQ=TTAATAATTGCATGCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:927:11:7,4:352,563:915,11:0.0119:2,2:51.4:1:35:0:0.11908:2.80:60:22:0.0119:0:1 0/0:984:4:0,4:367,611:978,4:0.0041:2,0:43.8:1:35:0:0.30307:0:60:8:0.0041:0:1
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chr2 58453844 58453844 A - intron FANCL NM_001114636:exon4:c.273+19T>-;NM_018062:exon4:c.273+19T>- . . rs755748731 ID=COSV52075517;OCCURENCE=3(large_intestine),3(biliary_tract) . . . . . . . 0.0946 0.0928 0.1898 0.0651 0.1102 0.0649 0.0905 0.1011 0.0810 0.0016 0.0031 0.0029 0 0 0.0027 0.0008 0.0012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2p16.1 0.5 225 820 chr2 58453843 . GA G 225 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=813;VD=92;AF=0.1132;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.01568;SOR=1.45739;LSEQ=GCAGTATGGTAACAGTGTCA;RSEQ=AAAAAAAAAAATTCTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:813:92:61,31:501,214:715,92:0.1132:2,2:35.2:1:34.6:1:0.47104:1.18947:60:184:0.1136:0.0197:0.2 0/1:820:66:43,23:479,273:752,66:0.0805:2,2:41.2:1:35:1:0.89402:1.07:60:132:0.0809:0.0073:0.1
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chr2 111884593 111884593 T - intronic BCL2L11 . . . rs59854799 . . . . . . 0.564297 0.6012 . . . . . . . . . 0.6170 0.8214 0.3602 0.3940 0.5966 0.5410 0.5441 0.5051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q13 1 384 2173 chr2 111884592 . CT C 384 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2155;VD=2054;AF=0.9531;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2122;SOR=0.87871;LSEQ=AACACTGTTTTCATATTTTC;RSEQ=TTTATGTCTCTGATTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2155:2054:1215,839:64,36:100,2054:0.9531:2,2:39.5:1:34.9:1:0.35009:1.2275:60:1026:0.954:0.0724:0.1 1/1:2173:2083:1253,830:59,29:88,2083:0.9586:2,2:39.6:1:34.9:1:0.22125:1.34748:60:4166:0.9595:0.0607:0.1
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chr2 128046944 128046946 TCT - exonic ERCC3 . nonframeshift deletion ERCC3:NM_000122:exon6:c.789_791del:p.E264del,ERCC3:NM_001303416:exon6:c.597_599del:p.E200del,ERCC3:NM_001303418:exon6:c.597_599del:p.E200del rs761456808 . . . . . . . . 0.0047 0.0014 0.0011 0.0014 0.0010 0.0005 0.0018 0.0044 0.0009 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q14.3 0.5 226 2569 chr2 128046943 . CTCT C 226 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2586;VD=74;AF=0.0286;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.12358;SOR=0.8209;LSEQ=TCAAAAGACACTGTCTGTGT;RSEQ=TCTTCTTCTTCTTCATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2586:74:44,30:1403,1106:2509,74:0.0286:2,2:41.6:1:35:1:0.63487:1.16:60:148:0.0287:0.0023:0.1 0/1:2569:89:47,42:1437,1040:2477,89:0.0346:2,2:40:1:34.9:1:0.32815:1.23463:60:178:0.0347:0.0023:0.1
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chr2 209101906 209101906 A - intron IDH1 NM_001282386:exon10:c.1155-13T>-;NM_001282387:exon10:c.1155-13T>-;NM_005896:exon10:c.1155-13T>- . . rs57383668 ID=COSV61616804;OCCURENCE=18(meninges),3(central_nervous_system),1(bone) . . . . . 0.982628 0.999 . 0.9903 0.9509 0.9900 0.9931 0.9973 0.9940 0.9930 0.9963 0.9861 0.9526 0.9964 1 1 1 0.9994 0.9938 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q34 1 347 1138 chr2 209101905 . GA G 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1182;VD=993;AF=0.8401;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.09629;SOR=0.85336;LSEQ=CGTTGCACACTAACGGGAAG;RSEQ=AAAAAAAAAGAAAATTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1182:993:466,527:78,94:172,993:0.8401:2,2:47.9:1:34.9:1:0.74081:1.07:60:992:0.8414:0.0144:0.1 1/1:1138:979:465,514:57,87:144,979:0.8603:2,2:46.6:1:34.9:1:0.08888:1.38:60:978:0.8602:0.0167:0.1
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chr2 209103969 209103969 - A intron IDH1 NM_001282386:exon9:c.992-12->T;NM_001282387:exon9:c.992-12->T;NM_005896:exon9:c.992-12->T . . rs751745975 ID=COSV61631870;OCCURENCE=1(large_intestine) . . . . . . . . 0.0002 0 9.952e-05 0.0001 0.0002 0.0004 0 0.0001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q34 0.25 134 1392 chr2 209103969 . G GA 134 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Insertion;DP=1428;VD=13;AF=0.0091;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.32923;SOR=0.79017;LSEQ=AAATGGAAGCTAAAAGAGGG;RSEQ=AAAAAAAACACAACACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1428:13:4,9:596,753:1349,13:0.0091:2,2:43.4:1:34.2:1:0.40817:1.78015:60:26:0.0101:0:0.1 0/1:1392:16:7,9:536,774:1310,16:0.0115:2,2:53.1:1:33.5:1:0.80429:1.12:60:15:0.0117:0:0.2
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chr2 209116299 209116299 - A splicing IDH1 NM_001282386:exon3:UTR5;NM_001282387:exon3:UTR5;NM_005896:exon3:UTR5 . . rs139018716 ID=COSV61646572;OCCURENCE=1(meninges),1(biliary_tract) . . . . . 0.0397364 0.005 0.0631 0.0206 0.1541 0.0141 0.0031 0.0020 0.0070 0.0111 0.0114 0.0446 0.1395 0.0087 0 0.0006 0.0018 0.0010 0.0082 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q34 0.5 214 1275 chr2 209116299 . G GA 214 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1297;VD=72;AF=0.0555;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03975;SOR=1.41042;LSEQ=GACTTCAATAAACCTAAAAA;RSEQ=AAAAAAAAAATACATGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1297:72:23,48:397,688:1085,72:0.0555:2,2:47.5:1:34.8:1:0.5257:1.20402:60:144:0.0682:0.0008:0.1 0/1:1275:51:15,36:393,690:1083,51:0.04:2,2:43.9:1:35:1:0.37162:1.3666:60:102:0.0478:0.0031:0.1
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chr2 212495336 212495336 - A intron ERBB4 NM_005235:exon17:c.1947-17->T;NM_001042599:exon17:c.1947-17->T . . rs112581570 ID=COSV53578726;OCCURENCE=1(breast),1(liver) 1257593 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . 0.1332 0.0481 0.2007 0.0484 0.0364 0.0105 0.0267 0.0265 0.0538 0.0590 0.1806 0.0233 0.0125 0.0020 0.0045 0.0030 0.0141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q34 0.5 230 1232 chr2 212495336 . G GA 230 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1287;VD=96;AF=0.0746;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.52687;SOR=0.9988;LSEQ=AGTTCTGACAACCAGAATGA;RSEQ=AAAAAAAAAAATAAAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1287:96:56,39:578,458:1036,96:0.0746:2,2:49:1:35:0:0.59018:1.14:60:192:0.1001:0:0.1 0/1:1232:92:54,38:505,420:925,92:0.0747:2,2:49.4:1:35:1:0.51007:1.18:60:184:0.1026:0.0016:0.2
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chr2 212530218 212530218 - A intron ERBB4 NM_005235:exon15:c.1717-16->T;NM_001042599:exon15:c.1717-16->T . . rs767387600 ID=COSV53600474;OCCURENCE=1(large_intestine) . . . . . . . 0.0034 0.0008 0.0006 0.0016 0.0008 0.0008 0.0007 0.0017 0.0008 0.0002 0 0.0012 0 0 0 0.0003 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q34 0.5 183 1564 chr2 212530218 . G GA 183 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1619;VD=38;AF=0.0235;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.13284;SOR=1.3681;LSEQ=GGACCCTGAAATGTGAAAAC;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1619:38:17,21:584,827:1411,38:0.0235:2,2:47.6:1:35:0:0.73952:1.15:60:76:0.0279:0:0.1 0/1:1564:27:9,17:592,783:1375,27:0.0173:2,2:43.9:1:34.6:1:0.43008:1.42777:60:54:0.02:0.0006:0.1
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chr2 212543924 212543924 A G intron ERBB4 NM_005235:exon13:c.1490-15T>C;NM_001042599:exon13:c.1490-15T>C . . rs4673628 ID=COSV53526947;OCCURENCE=2(lung) 1199895 Amyotrophic_lateral_sclerosis_19|not_specified|not_provided MONDO:MONDO:0014223,MedGen:C3715155,OMIM:615515|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.344249 0.0089 0.4735 0.3906 0.5191 0.3351 0.0125 0.3756 0.4447 0.3928 0.3658 0.4368 0.5163 0.3553 0.5433 0.0148 0.3996 0.4495 0.4035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q34 0.5 334 1838 chr2 212543924 . A G 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1814;VD=848;AF=0.4675;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4767;SOR=0.99394;LSEQ=CAGCAGCTGTGAAACACCAA;RSEQ=ATCAAGGGGAAATAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1814:848:430,418:504,460:964,848:0.4675:2,2:43.3:1:34.2:1:0.50992:1.06503:60:52:0.4633:0.0121:1.4 0/1:1838:862:482,380:538,434:972,862:0.469:2,2:42.8:1:34.3:1:0.81403:1.02:60:56.467:0.4659:0.0136:1.3
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chr2 215593233 215593233 T C UTR3 BARD1 NM_001282543:c.*167A>G;NM_001282549:c.*167A>G;NM_001282548:c.*167A>G;NM_001282545:c.*167A>G;NM_000465:c.*167A>G . . rs5020511 . 1213667 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.599241 0.3978 . . . . . . . . . 0.6634 0.7676 0.5243 0.6192 0.4391 0.6967 0.6304 0.6395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 301 1015 chr2 215593233 . T C 301 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=970;VD=444;AF=0.4577;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08147;SOR=1.13908;LSEQ=CAGCTTCTAAATGGTAAACA;RSEQ=AACATGAATTCCTAATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:444:311,133:338,188:526,444:0.4577:2,2:41.9:1:34.3:1:0.06439:1.30:60:73:0.4553:0.0103:1.1 0/1:1015:432:295,137:409,174:583,432:0.4256:2,2:41.7:1:34.1:1:0.53595:1.09153:60:71:0.4222:0:1.1
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chr2 215593261 215593261 - T UTR3 BARD1 NM_001282543:c.*138_*139insA;NM_001282549:c.*138_*139insA;NM_001282548:c.*138_*139insA;NM_001282545:c.*138_*139insA;NM_000465:c.*138_*139insA . . rs33960630 . 1282133 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.643171 0.6518 . . . . . . . . . 0.3738 0.2705 0.4959 0.3789 0.6282 0.3485 0.4010 0.3930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 301 1068 chr2 215593261 . C CT 301 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=995;VD=375;AF=0.3769;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.49162;SOR=1.00605;LSEQ=ATTCCTAATCTGGCATTAGA;RSEQ=TTTTTTTTTTTTTTTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:375:229,145:139,81:220,375:0.3769:2,2:45.8:1:34.9:1:0.6623:1.08641:60:750:1:0:0.4 0/1:1068:401:268,132:185,93:278,401:0.3755:2,2:48.1:1:34.9:1:0.93398:1.02:60:400:1:0:0.3
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chr2 215595164 215595164 G A exonic BARD1 . nonsynonymous SNV BARD1:NM_001282549:exon4:c.433C>T:p.R145C,BARD1:NM_001282548:exon5:c.562C>T:p.R188C,BARD1:NM_001282545:exon6:c.619C>T:p.R207C,BARD1:NM_001282543:exon9:c.1915C>T:p.R639C,BARD1:NM_000465:exon10:c.1972C>T:p.R658C rs3738888 ID=COSV53616840;OCCURENCE=1(pancreas) 140203 Malignant_tumor_of_breast|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|Triple-Negative_Breast_Cancer_Finding|not_specified|not_provided MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:C2348819|MedGen:CN169374|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity 0.00539137 0.0139 0.0059 0.0080 0.0019 0.0119 0.0112 0.0142 0.0081 0.0072 0.0048 0.0064 0.0031 0.0143 0 0.0086 0.0123 0.0065 0.0061 0.008 0.654 D 0.007 0.319 N 0.999 0.462 D 2.12 0.589 M 0.37 0.577 T -4.02 0.781 D -0.898 0.482 T 0.077 0.308 T . . . . . 0.978 0.769 D c 0.454 0.538 1.000 0.747 0.732 0.924 0 5.77 0.910 5.269 0.651 1.048 0.713 0.951 0.329 0.881 0.369 19.983 0.973 BRCT domain . . 2q35 0.5 319 1181 chr2 215595164 . G A 319 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1206;VD=577;AF=0.4784;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20428;SOR=0.93145;LSEQ=TCTGTTGAGCCTGCTTCTGC;RSEQ=TGGACCTTCAGGAATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1206:577:338,239:342,284:626,577:0.4784:2,2:41.3:1:34.7:1:0.18068:1.17:60:191.333:0.4795:0.005:1.1 0/1:1181:586:328,258:300,290:590,586:0.4962:2,2:42.1:1:34.7:1:0.07982:1.23:60:194.333:0.5013:0.0237:1.1
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chr2 215595645 215595645 C T intronic BARD1 . . . rs16852600 ID=COSV53612285;OCCURENCE=3(haematopoietic_and_lymphoid_tissue),1(lung) . . . . . 0.275359 0.3125 . 0.3787 0.1815 0.2606 0.3099 0.4126 0.3272 0.3706 0.4059 0.2824 0.1627 0.2392 0.37 0.3668 0.4048 0.3106 0.3523 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 329 1413 chr2 215595645 . C T 329 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1419;VD=667;AF=0.47;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31436;SOR=0.96153;LSEQ=CACTTACCATCTATACTGCT;RSEQ=ATTTTGACAGTTATATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1419:667:348,319:401,349:750,667:0.47:2,2:42.8:1:35:1:0.63176:1.05318:60:1334:0.4741:0.0099:1.2 0/1:1413:678:343,335:388,347:735,678:0.4798:2,2:41.4:1:35:1:0.42433:1.09201:60:1356:0.4809:0.0064:1.3
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chr2 215614507 215614508 TT - intronic BARD1 . . . rs397987744 . . . . . . 0.530152 0.6071 . . . . . . . . . 0.4834 0.5192 0.5721 0.5 0.5644 0.4750 0.4518 0.4504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 317 1422 chr2 215614506 . CTT C 317 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1416;VD=549;AF=0.3877;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=0.33132;SOR=1.03735;LSEQ=TTAATAAAGAAAAAAACAAC;RSEQ=TTTTTTTTTTTAATGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1416:549:308,241:308,174:482,549:0.3877:2,2:42.4:1:34.9:1:0.01101:1.3846:60:1098:0.3891:0.0191:0.1 0/1:1422:539:310,229:276,213:489,539:0.379:2,2:42.3:1:34.8:1:0.75262:1.04:60:1078:0.3798:0.0169:0.1
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chr2 215632192 215632192 G A intron BARD1 NM_001282543:exon5:c.1511+14C>T;NM_000465:exon6:c.1568+14C>T . . rs5031011 ID=COSV53615058;OCCURENCE=2(haematopoietic_and_lymphoid_tissue) 250542 Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.352236 0.3433 0.3353 0.3633 0.3420 0.2795 0.3694 0.4537 0.3613 0.3786 0.3987 0.3655 0.3481 0.2938 0.4073 0.3850 0.4501 0.3537 0.4131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 308 1217 chr2 215632192 . G A 308 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1110;VD=414;AF=0.373;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51568;SOR=0.99967;LSEQ=ATTTTAAAAATAATTTTTAC;RSEQ=TTGAACTACTTACACAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1110:414:292,122:485,211:696,414:0.373:2,2:26.1:1:34.9:1:0.78674:1.04:60:413:0.3751:0.0387:2.7 0/1:1217:454:343,111:524,239:763,454:0.373:2,2:28.5:1:35:1:0.01069:1.41:60:908:0.3746:0.0197:2.7
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chr2 215632255 215632256 CA TG exonic BARD1 . nonframeshift substitution BARD1:NM_001282543:exon5:c.1461_1462delinsCA:p.V488M,BARD1:NM_000465:exon6:c.1518_1519delinsCA:p.V507M rs386654966 . 212134 Breast_carcinoma|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 333 1706 chr2 215632255 . CA TG 333 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Complex;DP=1627;VD=702;AF=0.4315;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45833;SOR=1.00982;LSEQ=TAACAGCTTGACTATATCCA;RSEQ=TGCCCATTCTTGGCTGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1627:702:375,327:515,389:904,702:0.4315:2,2:41.1:1:35:1:0.15695:1.15434:60:1404:0.4331:0.0295:1.3 0/1:1706:732:420,312:540,417:957,732:0.4291:2,2:42.8:1:35:1:0.72863:1.04:60:1464:0.4311:0.0264:1.3
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chr2 215632256 215632256 A G exonic BARD1 . synonymous SNV BARD1:NM_001282543:exon5:c.1461T>C:p.H487H,BARD1:NM_000465:exon6:c.1518T>C:p.H506H rs2070093 ID=COSV53617490;OCCURENCE=1(urinary_tract) 181790 Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.770567 0.9484 0.7138 0.8148 0.5943 0.8257 0.9540 0.8980 0.8109 0.8343 0.8414 0.7658 0.6055 0.7883 0.7848 0.9543 0.8947 0.8028 0.8286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 341 1659 chr2 215632256 . A G 341 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1575;VD=914;AF=0.5803;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47622;SOR=1.00682;LSEQ=AACAGCTTGACTATATCCAC;RSEQ=TGCCCATTCTTGGCTGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1575:914:512,402:0,0:0,914:0.5803:0,2:38.4:1:34.3:1:1:0:60:75.167:0.9967:0.0038:1.1 1/0:1659:960:544,416:3,2:5,960:0.5787:2,2:39.5:1:34.5:1:1:1.14687:60:319:0.9907:0.0066:1.1
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chr2 215634055 215634055 C T intron BARD1 NM_001282543:exon4:c.1258-19G>A;NM_000465:exon5:c.1315-19G>A . . rs6704780 ID=COSV53612311;OCCURENCE=2(haematopoietic_and_lymphoid_tissue) 250543 Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.365216 0.3433 0.3595 0.3829 0.3735 0.2861 0.3740 0.4756 0.3863 0.3913 0.4085 0.3855 0.3717 0.3110 0.4267 0.3835 0.4670 0.3754 0.4284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 324 1203 chr2 215634055 . C T 324 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1243;VD=670;AF=0.539;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28968;SOR=1.04935;LSEQ=CCCTAGAAAAATGAACAAAA;RSEQ=GGAAATTAAAAAGCATTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1243:670:325,345:295,277:572,670:0.539:2,2:38.8:1:34.6:1:0.30551:1.13041:60:166.5:0.5491:0.0233:1.1 1/0:1203:634:315,319:284,285:569,634:0.527:2,2:40.5:1:34.8:1:0.95398:1.00914:60:1268:0.5314:0.0175:1.1
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chr2 215645464 215645464 C G exonic BARD1 . nonsynonymous SNV BARD1:NM_001282543:exon3:c.1077G>C:p.R359S,BARD1:NM_000465:exon4:c.1134G>C:p.R378S rs2229571 ID=COSV53612030;OCCURENCE=1(large_intestine),2(haematopoietic_and_lymphoid_tissue),1(lung) 152483 Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.459265 0.3413 0.5318 0.5456 0.3957 0.3974 0.3674 0.6939 0.6251 0.5605 0.4911 0.5519 0.4006 0.4376 0.5894 0.3851 0.6827 0.6283 0.6214 0.174 0.225 T 0.079 0.210 N 1 0.090 P 1.67 0.430 L -0.67 0.725 T -0.31 0.121 N -0.921 0.454 T 0.000 0.000 T . . . . . 0.121 0.168 N c -1.031 -1.061 0.007 0.115 0.672 0.522 0 -1.03 0.095 -0.395 0.073 0.935 0.490 0.000 0.063 0.050 0.164 2.531 0.044 . ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000229267.2|ENSG00000138376.6|ENSG00000229267.2|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6 Adipose_Subcutaneous|Artery_Aorta|Artery_Tibial|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Heart_Atrial_Appendage|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Testis|Thyroid|Whole_Blood 2q35 0.5 348 2252 chr2 215645464 . C G 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2318;VD=1141;AF=0.4922;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10616;SOR=1.07852;LSEQ=TCGGACATGTTACTGTTTTT;RSEQ=CTCCCTGATGTACCACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2318:1141:658,483:690,480:1170,1141:0.4922:2,2:35.3:1:34.3:1:0.52709:1.05513:60:113.1:0.4943:0.0216:1.1 0/1:2252:1066:604,462:692,488:1180,1066:0.4734:2,2:34.8:1:34.5:1:0.34705:1.08461:60:117.444:0.4751:0.016:1.1
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chr2 215663497 215663497 A - intronic BARD1 . . . rs10707828 . . . . . . . . . . . . . . . . . 0.6979 0.7095 0.7222 0.7130 0.9467 0.4300 0.6763 0.7156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 0.5 265 421 chr2 215663496 . GA G 265 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=465;VD=196;AF=0.4215;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.14838;SOR=1.1647;LSEQ=AATAACCACTATTAAAAAAA;RSEQ=AAAAAAAAAAAAAAAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:196:107,89:85,108:193,196:0.4215:2,2:46.2:1:34.9:1:0.04264:1.53:60:392:0.4289:0.0022:0.3 0/1:421:162:93,69:102,80:182,162:0.3848:2,2:45.3:1:34.9:1:0.82793:1.06:60:324:0.3894:0.0048:0.3
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chr2 215674224 215674224 G A exonic BARD1 . nonsynonymous SNV BARD1:NM_000465:exon1:c.70C>T:p.P24S,BARD1:NM_001282543:exon1:c.70C>T:p.P24S,BARD1:NM_001282545:exon1:c.70C>T:p.P24S,BARD1:NM_001282548:exon1:c.70C>T:p.P24S,BARD1:NM_001282549:exon1:c.70C>T:p.P24S rs1048108 ID=COSV53608734;OCCURENCE=3(lung),1(thyroid),1(large_intestine) 181856 Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.33127 0.3313 0.3031 0.4427 0.2861 0.4864 0.4163 0.4866 0.4509 0.4413 0.4413 0.3408 0.2121 0.4141 0.41 0.3779 0.4177 0.3819 0.4378 0.184 0.912 T 0.000 0.447 D 0.608 0.588 P 1.195 0.303 L -0.72 0.849 T -1.19 0.303 N -1.043 0.165 T 0.000 0.000 T . . . . . 0.263 0.227 N c -0.507 -0.404 1.000 0.747 0.442 0.072 0 3.1 0.346 0.990 0.290 0.880 0.385 0.726 0.286 0.116 0.195 5.315 0.151 . ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000229267.2|ENSG00000229267.2|ENSG00000229267.2|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6 Adipose_Subcutaneous|Adrenal_Gland|Artery_Aorta|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Esophagus_Mucosa|Heart_Atrial_Appendage|Heart_Left_Ventricle|Lung|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Stomach|Testis|Thyroid 2q35 0.5 350 2603 chr2 215674224 . G A 350 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2860;VD=1371;AF=0.4794;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21144;SOR=0.95606;LSEQ=ACCATCCGGTTCCATGGCGG;RSEQ=CGCGGAACGAGGCTCGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2860:1371:730,641:761,723:1484,1371:0.4794:2,2:40.3:1:33.6:1:0.29409:1.08:60:38.171:0.4763:0.0056:1.7 0/1:2603:1277:652,625:670,637:1307,1277:0.4906:2,2:40.4:1:33.8:1:0.93727:1.00825:60:46.296:0.4896:0.0065:1.7
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chr2 215674323 215674323 C G intron BARD1 NM_001282543:c.-30G>C;NM_001282549:c.-30G>C;NM_001282548:c.-30G>C;NM_001282545:c.-30G>C;NM_000465:c.-30G>C . . rs1129804 . 287668 Familial_cancer_of_breast|not_provided MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.744609 0.7817 0.7709 0.7020 0.7822 0.8071 0.8144 0.8431 0.7267 0.6797 0.6717 0.7473 0.7567 0.7976 0.7233 0.8290 0.7739 0.7243 0.75 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 1 366 1330 chr2 215674323 . C G 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1561;VD=1559;AF=0.9987;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29146;SOR=0;LSEQ=TTCGGATGAAAGGCTCCTCG;RSEQ=AGAGCGGGAAGCAAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1561:1559:627,932:0,0:0,1559:0.9987:0,2:41.6:1:34.6:1:1:0:60:193.875:0.9994:0.0436:2.6 1/1:1330:1330:570,760:0,0:0,1330:1:0,2:43.2:1:34.5:1:1:0:60:132:1:0:2.6
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chr2 216212279 216212279 G C intronic ATIC . . . rs4673992 . . . . . . 0.946086 1 . . . . . . . . . 0.9255 0.9286 0.9200 0.8841 0.9963 0.8841 0.9276 0.9133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q35 1 355 1392 chr2 216212279 . G C 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1374;VD=1364;AF=0.9927;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30438;SOR=0.68948;LSEQ=TGCTGGATGGAAAACAGAAG;RSEQ=CTGCTAATCAAATACTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1374:1364:916,448:0,1:1,1364:0.9927:0,2:40.3:1:34:1:0.32894:0:60:44.467:0.9926:0.0233:1.1 1/1:1392:1385:940,445:0,0:0,1385:0.995:0,2:39.4:1:34.1:1:1:0:60:54.4:0.9956:0.0359:1.1
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chr2 234668879 234668879 - AT intronic UGT1A10;UGT1A3;UGT1A4;UGT1A5;UGT1A6;UGT1A7;UGT1A8;UGT1A9 . . . rs34983651 ID=COSV59387575;OCCURENCE=1(prostate) 27314 Gilbert_syndrome|Lucey-Driscoll_syndrome|Crigler-Najjar_syndrome,_type_II|Crigler-Najjar_syndrome_type_1|Bilirubin,_serum_level_of,_quantitative_trait_locus_1|Irinotecan_response|not_specified|not_provided MONDO:MONDO:0007745,MedGen:C0017551,OMIM:143500,SNOMED_CT:27503000|MONDO:MONDO:0009383,MedGen:C0270210,OMIM:237900,Orphanet:ORPHA2312,SNOMED_CT:47444008|MONDO:MONDO:0011725,MedGen:C2931132,OMIM:606785,Orphanet:ORPHA79235,SNOMED_CT:68067009|MONDO:MONDO:0021020,MedGen:CN029644,OMIM:218800,Orphanet:ORPHA79234|MedGen:C1866173,OMIM:601816|MedGen:CN077989|MedGen:CN169374|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity|_drug_response|_other 0.32528 0.129 . . . . . . . . . 0.3472 0.4032 0.3304 0.3056 0.1205 0.4020 0.3266 0.3856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2q37.1 0.5 320 1510 chr2 234668879 . C CAT 320 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1512;VD=571;AF=0.3776;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=0.35732;SOR=0.97025;LSEQ=GTGTATCGATTGGTTTTTGC;RSEQ=ATATATATATATATAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1512:571:338,232:440,263:703,571:0.3776:2,2:42.8:1:34.9:1:0.24764:1.14821:60:1142:0.8157:0.0278:0.1 0/1:1510:581:353,228:432,268:700,581:0.3848:2,2:46.8:1:34.9:1:0.72998:1.04113:60:580:0.8394:0:0.1
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chr3 14187449 14187449 G T exonic XPC . nonsynonymous SNV XPC:NM_001354726:exon15:c.2236C>A:p.Q746K,XPC:NM_001354727:exon16:c.2809C>A:p.Q937K,XPC:NM_001354729:exon16:c.2797C>A:p.Q933K,XPC:NM_001354730:exon16:c.2569C>A:p.Q857K,XPC:NM_004628:exon16:c.2815C>A:p.Q939K rs2228001 ID=COSV53207797;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) 187973 Xeroderma_pigmentosum,_group_C|Arrhythmogenic_right_ventricular_cardiomyopathy|Xeroderma_pigmentosum|not_specified|not_provided MONDO:MONDO:0010211,MedGen:C2752147,OMIM:278720,SNOMED_CT:25784009|MONDO:MONDO:0016587,MedGen:C0349788,Orphanet:ORPHA247,SNOMED_CT:253528005,SNOMED_CT:281170005|MONDO:MONDO:0019600,MedGen:C0043346,Orphanet:ORPHA910,SNOMED_CT:44600005|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.684704 0.6667 0.6421 0.6366 0.7265 0.7100 0.6432 0.7090 0.5931 0.6540 0.6510 0.6556 0.7228 0.7057 0.5629 0.6382 0.6985 0.6087 0.6337 1.0 0.010 T 0.000 0.629 N 1.000 0.090 P -2.455 0.001 N 1.93 0.229 T 1.67 0.006 N -0.955 0.400 T 0.000 0.000 T . . . . . 0.059 0.117 N c -0.971 -0.646 1.000 0.747 0.722 0.854 0 4.24 0.493 2.828 0.476 0.115 0.208 1.000 0.715 0.998 0.697 7.925 0.289 . ENSG00000233121.1|ENSG00000233121.1|ENSG00000228242.3|ENSG00000228242.3|ENSG00000163528.8|ENSG00000163528.8|ENSG00000163528.8|ENSG00000170860.3 Artery_Tibial|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Left_Ventricle|Muscle_Skeletal|Muscle_Skeletal 3p25.1 0.5 349 2031 chr3 14187449 . G T 349 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2108;VD=1026;AF=0.4867;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34554;SOR=1.02703;LSEQ=TGGGCGCTCAGCTCACAGCT;RSEQ=CTCAAATGGGAACAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2108:1026:526,500:512,559:1071,1026:0.4867:2,2:40.3:1:34.9:1:0.11594:1.15:60:2052:0.4914:0.0138:1.4 0/1:2031:975:508,467:531,521:1052,975:0.4801:2,2:40.8:1:34.7:1:0.47691:1.07:60:242.75:0.4819:0.0167:1.4
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chr3 37067097 37067097 A T intron MLH1 NM_001167619:exon11:c.316-31A>T;NM_001167618:exon12:c.316-31A>T;NM_001167617:exon12:c.745-31A>T;NM_001354622:exon11:c.16-31A>T;NM_001354619:exon13:c.316-31A>T;NM_001354628:exon12:c.1039-31A>T;NM_001354629:exon11:c.940-31A>T;NM_001354615:exon11:c.316-31A>T;NM_001354616:exon11:c.316-31A>T;NM_001354630:exon12:c.1039-31A>T;NM_001354625:exon9:UTR5;NM_001354621:exon10:c.16-31A>T;NM_000249:exon12:c.1039-31A>T;NM_001258274:exon13:c.316-31A>T;NM_001258273:exon11:c.316-31A>T;NM_001354627:exon10:UTR5;NM_001354623:exon10:c.16-31A>T;NM_001354626:exon10:UTR5;NM_001354618:exon12:c.316-31A>T;NM_001354624:exon10:UTR5;NM_001354617:exon12:c.316-31A>T;NM_001258271:exon12:c.1039-31A>T;NM_001354620:exon12:c.745-31A>T . . rs59684491 ID=COSV51624244;OCCURENCE=1(skin) 619191 Hereditary_cancer-predisposing_syndrome|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . . 0.0552 0.1 0 0.1667 . 0.0706 0.1 0.0474 0.2230 0.2861 0.2527 0.2763 0.3419 0.0408 0.1798 0.2076 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3p22.2 0.5 164 262 chr3 37067097 . A T 164 PASS STATUS=AFDiff;SAMPLE=NCCL202312;TYPE=SNV;DP=193;VD=21;AF=0.1088;SHIFT3=0;MSI=12.000;MSILEN=2;SSF=0.42796;SOR=1.10798;LSEQ=ATATATATATATATATATAT;RSEQ=TATTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:21:16,5:103,36:139,21:0.1088:2,2:45.8:1:35:0:1:1.12:60:42:0.1167:0:2.1 0/1:262:26:13,13:141,49:190,26:0.0992:2,2:34.7:1:35:0:0.01882:2.86134:60:52:0.1066:0:2.2
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chr3 41268676 41268676 - AT intron CTNNB1 NM_001098210:exon7:c.937-23->AT;NM_001904:exon7:c.937-23->AT;NM_001098209:exon7:c.937-23->AT;NM_001330729:exon8:c.916-23->AT . . rs765762484 . . . . . . . . . 0.0017 0.0024 0.0012 0.0019 0.0002 0.0012 0 0.0040 0.0012 0.0031 0.0012 0 0.0012 0 0.0005 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3p22.1 0.5 164 1002 chr3 41268676 . G GAT 164 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=957;VD=26;AF=0.0272;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.32543;SOR=1.18861;LSEQ=CAAGATTCCTTGACTAACAA;RSEQ=ATATATATATATATCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:957:26:17,8:540,240:780,26:0.0272:2,2:35.8:1:35:1:1:1.05875:60:52:0.0338:0.0021:0.1 0/1:1002:23:17,6:553,264:817,23:0.023:2,2:39.3:1:34.9:1:0.65345:1.35:60:46:0.0284:0.003:0.1
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chr3 142168331 142168331 C T exonic ATR . synonymous SNV ATR:NM_001354579:exon46:c.7683G>A:p.Q2561Q,ATR:NM_001184:exon47:c.7875G>A:p.Q2625Q rs1802904 ID=COSV99377126;OCCURENCE=17(meninges) 99572 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.916334 0.9266 0.8978 0.8634 0.9730 0.7539 0.9303 0.8134 0.8427 0.8415 0.9349 0.8880 0.9702 0.7775 0.8079 0.9420 0.7995 0.8651 0.8510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 1 373 1675 chr3 142168331 . C T 373 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1679;VD=1672;AF=0.9958;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27543;SOR=0.57187;LSEQ=AAGTTTTCATCAGTAGCTTC;RSEQ=TGTATAAGGTAATGCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1679:1672:1005,667:0,0:0,1672:0.9958:0,2:37:1:34.9:1:1:0:60:1671:0.9964:0.0298:1.1 1/1:1675:1671:1023,648:1,0:1,1671:0.9976:0,2:37:1:35:1:1:0:60:3342:0.9982:0.0233:1.1
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chr3 142178144 142178144 C T exonic ATR . nonsynonymous SNV ATR:NM_001354579:exon42:c.7082G>A:p.R2361Q,ATR:NM_001184:exon43:c.7274G>A:p.R2425Q rs2229032 ID=COSV63383988;OCCURENCE=6(meninges),1(stomach),3(haematopoietic_and_lymphoid_tissue),2(kidney),12(soft_tissue),1(thyroid),1(upper_aerodigestive_tract) 140173 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.102236 0.1012 0.1342 0.1313 0.0804 0.0951 0.1039 0.1665 0.1579 0.1546 0.0939 0.1332 0.0813 0.1160 0.0728 0.1017 0.1746 0.1584 0.1469 0.56 0.064 T 0.249 0.155 N 0.998 0.224 P 0.615 0.157 N -1.0 0.760 T 0.04 0.065 N -1.105 0.035 T 0.001 0.002 T . . . . . 0.231 0.218 N c -1.517 -1.496 0.999 0.388 0.706 0.609 0 -9.12 0.006 0.037 0.136 -1.656 0.008 0.961 0.334 0.958 0.437 19.102 0.932 Phosphatidylinositol 3-/4-kinase, catalytic domain ENSG00000120756.8 Artery_Aorta 3q23 0.5 351 2227 chr3 142178144 . C T 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2135;VD=1059;AF=0.496;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23273;SOR=1.04716;LSEQ=GCCTGGGCAGGAGAAATTCT;RSEQ=GGAATACTTTGAGTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2135:1059:561,498:550,524:1074,1059:0.496:2,2:38:1:34.9:1:0.43531:1.07:60:2118:0.5014:0.0323:1.1 0/1:2227:1079:553,526:644,502:1146,1079:0.4845:2,2:38.3:1:34.9:1:0.02158:1.22012:60:2158:0.488:0.0296:1.1
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chr3 142188337 142188337 A C exonic ATR . nonsynonymous SNV ATR:NM_001354579:exon37:c.6202T>G:p.Y2068D,ATR:NM_001184:exon38:c.6394T>G:p.Y2132D rs28910273 ID=COSV63384218;OCCURENCE=1(soft_tissue) 167847 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.00199681 . 0.0052 0.0030 0.0017 0.0017 0 0.0009 0.0047 0.0029 0.0014 0.0028 0.0017 0.0012 0 0 0.0014 0.0043 0.0010 0.062 0.369 T 0.205 0.165 N 0.997 0.228 N -1.2 0.008 N 3.63 0.044 T 0.99 0.014 N -0.903 0.477 T 0.004 0.012 T 0.011 0.278 T . . 0.826 0.415 D c -0.866 -0.711 0.013 0.124 0.706 0.609 0 0.823 0.179 2.404 0.439 -0.124 0.112 1.000 0.715 0.590 0.287 9.330 0.370 Armadillo-type fold|PIK-related kinase . . 3q23 0.5 336 2002 chr3 142188337 . A C 336 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1959;VD=962;AF=0.4911;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43912;SOR=0.98831;LSEQ=AAATTGATATGGAGCTAAAT;RSEQ=GTTTGTATGCTCTGTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1959:962:517,445:518,476:994,962:0.4911:2,2:38.3:1:33.5:1:0.49679:1.07:60:29.062:0.4831:0.0184:1.1 0/1:2002:989:516,473:549,456:1005,989:0.494:2,2:40.3:1:33.8:1:0.28141:1.10356:60:34.321:0.4873:0.0125:1.1
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chr3 142215171 142215171 T C intron ATR NM_001354579:exon33:c.5706+32A>G;NM_001184:exon34:c.5898+32A>G . . rs11719960 ID=COSV63384221;OCCURENCE=5(soft_tissue) 167845 not_specified MedGen:CN169374 no_assertion_criteria_provided Likely_benign . . 0.0026 0.0566 0.0033 0.0375 0.0609 0.0517 0.0957 0.0985 0.0410 0.0286 0.0080 0.0116 0.0059 0.0196 0.0280 0.0442 0.0266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 1 239 170 chr3 142215171 . T C 239 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=133;VD=118;AF=0.8872;SHIFT3=7;MSI=19.000;MSILEN=2;SSF=0.36472;SOR=0.81787;LSEQ=TATATATATATATATATATA;RSEQ=ATATATATGATGACATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:133:118:84,34:11,4:15,118:0.8872:2,2:26.5:1:32.3:1:1:1.11223:60:12.111:0.8862:0.1729:2.1 1/1:170:154:103,51:12,4:16,154:0.9059:2,2:31.4:1:33:1:0.58703:1.48219:60:18.25:0.9012:0.1235:2.1
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chr3 142215178 142215178 A C intron ATR NM_001354579:exon33:c.5706+25T>G;NM_001184:exon34:c.5898+25T>G . . rs7620648 ID=COSV63391396;OCCURENCE=1(liver) 167844 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign . . 0.6140 . . . . . . . . 0.6677 0.7981 0.5208 0.6102 0.5442 0.7070 0.6159 0.6328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.75 246 227 chr3 142215178 . A C 246 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=224;VD=170;AF=0.7589;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0.16231;SOR=0.77883;LSEQ=ATATATATATATATATATAT;RSEQ=TGATGACATTTCCCTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:170:129,41:49,4:53,170:0.7589:2,2:22.8:1:33.2:1:0.00989:3.87492:60:33:0.7534:0.125:1.8 1/1:227:182:128,54:40,5:45,182:0.8018:2,2:31.8:1:32.8:1:0.01274:3.36023:60:19.222:0.7936:0:2
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chr3 142217537 142217537 A G exonic ATR . synonymous SNV ATR:NM_001354579:exon31:c.5268T>C:p.Y1756Y,ATR:NM_001184:exon32:c.5460T>C:p.Y1820Y rs2227932 ID=COSV100637634;OCCURENCE=4(meninges) 140174 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.066893 0.003 0.0768 0.0946 0.0164 0.0368 0.0015 0.1258 0.1091 0.0942 0.1611 0.0814 0.0205 0.0489 0.0894 0 0.1276 0.1158 0.0949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 341 1925 chr3 142217537 . A G 341 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1892;VD=938;AF=0.4958;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5083;SOR=1.00075;LSEQ=CTCACTAGTTTCAGTGAGTC;RSEQ=TAAAAAGCTGTGATATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1892:938:511,427:479,474:953,938:0.4958:2,2:38.1:1:34.6:1:0.07251:1.18:60:186.6:0.495:0.0169:1.1 0/1:1925:954:522,432:529,440:969,954:0.4956:2,2:37.7:1:34.5:1:0.96349:1.01:60:105:0.4937:0.0197:1.1
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chr3 142231063 142231063 A - intron ATR NM_001354579:exon26:c.4660+39T>-;NM_001184:exon27:c.4852+39T>- . . rs776838660 ID=COSV63383872;OCCURENCE=13(ovary),1(biliary_tract) 1276305 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.1329 0.1118 0.0978 0.1545 0.2682 0.1352 0.1336 0.1083 0.0048 0.0011 0.0220 0 0.0007 0.1136 0.0031 0.0060 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 305 1535 chr3 142231062 . TA T 305 PASS STATUS=AFDiff;SAMPLE=NCCL202312;TYPE=Deletion;DP=1654;VD=443;AF=0.2678;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.00101;SOR=1.29539;LSEQ=AGAGCTAATTGGTGAATAGC;RSEQ=AAAAAAAAAAAAAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1654:443:288,155:585,290:875,443:0.2678:2,2:38.9:1:34.7:1:0.53758:1.0856:60:220.5:0.2673:0.0345:0.2 0/1:1535:338:225,113:585,285:870,338:0.2202:2,2:43.7:1:35:1:0.83807:1.03088:60:676:0.2206:0.0007:0.1
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chr3 142259707 142259707 A - intron ATR NM_001354579:exon17:c.3389+39T>-;NM_001184:exon18:c.3581+39T>- . . rs201551475 . 1215526 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.4537 0.4433 0.4430 0.4386 0.4703 0.4581 0.4803 0.4529 0.1962 0.1635 0.2229 0.1092 0.1110 0.4273 0.1971 0.2252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 322 1188 chr3 142259706 . CA C 322 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1412;VD=607;AF=0.4299;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.06563;SOR=1.13179;LSEQ=GTTAGTGCTACTGGAAAATG;RSEQ=AAAAAAAAAAAAATTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1412:607:411,196:463,195:658,607:0.4299:2,2:37.2:1:34.9:1:0.32998:1.13218:60:1214:0.4302:0.068:0.2 0/1:1188:475:330,145:434,155:589,475:0.3998:2,2:43.5:1:35:1:0.13222:1.23005:60:950:0.4012:0.0034:0.1
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chr3 142266771 142266771 A - intron ATR NM_001354579:exon15:c.2980-19T>-;NM_001184:exon16:c.3172-19T>- . . rs574734712 . . . . . . 0.000998403 . 0.0403 0.0012 0.0004 0.0007 0 0.0003 0.0005 0.0015 0.0054 0.0002 0.0001 0 0 0 0 0.0002 0.0010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.25 136 1354 chr3 142266770 . TA T 136 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1411;VD=15;AF=0.0106;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04724;SOR=2.41349;LSEQ=ATTCTAACCCAAAGACATGT;RSEQ=AAAAAAATTTTTTTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1411:15:4,11:530,865:1395,15:0.0106:2,2:31.7:1:35:1:0.43379:1.68439:60:30:0.0107:0.0028:0.3 0/0:1354:6:4,2:466,882:1348,6:0.0044:2,2:39.5:1:35:0:0.19081:3.78:60:12:0.0044:0:0.2
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chr3 142274739 142274739 - T exonic ATR . frameshift insertion ATR:NM_001354579:exon9:c.2128dupA:p.I710Nfs*3,ATR:NM_001184:exon10:c.2320dupA:p.I774Nfs*3 rs778867790 ID=COSV63384207;OCCURENCE=1(breast),1(liver),1(large_intestine),8(prostate),5(endometrium) 931793 not_provided MedGen:CN517202 criteria_provided,_single_submitter Pathogenic . . . 0.0036 0.0027 0.0008 0.0004 0.0002 0.0023 0.0048 0.0151 6.653e-05 0.0001 0 0 0 0 6.797e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 232 1876 chr3 142274739 . A AT 232 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1923;VD=93;AF=0.0484;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.22196;SOR=0.88389;LSEQ=CAAGTTTTACTGGACTAGGT;RSEQ=TTTTTTTTTTCAGTAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1923:93:64,28:956,665:1621,93:0.0484:2,2:43.2:1:35:0:0.04916:1.59:60:186:0.0575:0:0.1 0/1:1876:102:51,50:942,627:1569,102:0.0544:2,2:40.5:1:34.8:1:0.06052:1.47255:60:204:0.0651:0.0048:0.1
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chr3 142277424 142277427 ATAA - splicing ATR NM_001354579:exon7:r.spl;NM_001184:exon8:r.spl . . rs764936051 . 1283081 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . 0.1935 0.0408 0.0807 0.0468 0.0366 0.0588 0.0375 0.0489 0.0188 0.0092 0.0284 0.0050 0 0 0.0055 0.0005 0.0042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.25 189 944 chr3 142277423 . GATAA G 189 p8 STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=909;VD=46;AF=0.0506;SHIFT3=5;MSI=6.000;MSILEN=4;SSF=0;SOR=25.08121;LSEQ=GATAGATAGATAGATAGATA;RSEQ=ATAAAACAAACCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:909:46:41,5:561,302:863,46:0.0506:2,2:5.1:1:34.3:1:0.00037:4.41:60:92:0.0507:0.0473:1.8 0/0:944:2:1,1:614,328:942,2:0.0021:2,2:40:1:35:0:1:1.8707:60:4:0.0021:0:0
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chr3 142277427 142277427 A G intron ATR NM_001354579:exon7:c.1693+39T>C;NM_001184:exon8:c.1885+39T>C . . rs73240318 ID=COSV63383992;OCCURENCE=8(haematopoietic_and_lymphoid_tissue),2(lung),1(large_intestine),3(central_nervous_system),1(biliary_tract) 167814 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.11222 0.1012 0.1402 0.0739 0.0178 0.0316 0.0651 0.0888 0.0921 0.0913 0.0674 0.1045 0.0645 0.0783 0.0582 0.0905 0.1217 0.1268 0.1195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 305 1023 chr3 142277427 . A G 305 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=899;VD=399;AF=0.4438;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.33531;SOR=0.9576;LSEQ=GATAGATAGATAGATAGATA;RSEQ=ATAAAACAAACCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:899:399:254,145:336,160:496,399:0.4438:2,2:33.4:1:33.9:1:0.20256:1.19857:60:43.333:0.4412:0:1.1 0/1:1023:465:304,161:369,183:552,465:0.4545:2,2:32.3:1:34.5:1:0.64171:1.06782:60:154:0.4552:0.0371:1.2
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chr3 142277575 142277575 A T exonic ATR . synonymous SNV ATR:NM_001354579:exon7:c.1584T>A:p.G528G,ATR:NM_001184:exon8:c.1776T>A:p.G592G rs2227930 ID=COSV63383320;OCCURENCE=1(stomach),1(haematopoietic_and_lymphoid_tissue),20(soft_tissue),1(pancreas),14(meninges),2(large_intestine),3(central_nervous_system) 167812 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.598043 0.4732 0.6630 0.5470 0.8042 0.4371 0.4656 0.5537 0.5710 0.5605 0.4360 0.6300 0.7950 0.4976 0.5728 0.4851 0.5406 0.5824 0.5704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 348 1950 chr3 142277575 . A T 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2015;VD=1038;AF=0.5151;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02347;SOR=1.13683;LSEQ=ATCCATGGAAGTGAGAGCAT;RSEQ=CCACATAAATCTTCCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2015:1038:608,430:541,432:973,1038:0.5151:2,2:38.4:1:34.8:1:0.19106:1.13:60:1037:0.5157:0.0278:1.1 0/1:1950:942:524,418:534,472:1006,942:0.4831:2,2:39.2:1:34.8:1:0.27477:1.11:60:941:0.4831:0.0231:1.1
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chr3 142281612 142281612 A G exonic ATR . nonsynonymous SNV ATR:NM_001184:exon4:c.632T>C:p.M211T,ATR:NM_001354579:exon4:c.632T>C:p.M211T rs2227928 ID=COSV63383325;OCCURENCE=14(meninges),3(large_intestine),1(biliary_tract),1(stomach),1(haematopoietic_and_lymphoid_tissue),20(soft_tissue),4(prostate) 99571 Seckel_syndrome_1|not_specified|not_provided MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.597444 0.4732 0.6623 0.5480 0.8021 0.4387 0.4670 0.5544 0.5719 0.5607 0.4387 0.6291 0.7916 0.4964 0.5728 0.4845 0.5404 0.5832 0.5708 1.0 0.010 T 0.299 0.146 N 1.000 0.090 P 0.145 0.088 N -0.14 0.650 T -0.2 0.102 N -0.930 0.442 T 0.000 0.000 T . . . . . 0.108 0.160 N c -0.764 -0.533 0.498 0.209 0.651 0.465 0 4.6 0.564 1.477 0.348 -0.247 0.091 0.937 0.323 0.958 0.437 4.074 0.093 Armadillo-like helical ENSG00000175054.10|ENSG00000114127.6|ENSG00000175054.10|ENSG00000272565.1|ENSG00000114127.6 Adipose_Subcutaneous|Brain_Cerebellar_Hemisphere|Nerve_Tibial|Thyroid|Thyroid 3q23 0.5 353 2521 chr3 142281612 . A G 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2443;VD=1213;AF=0.4965;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27199;SOR=1.03674;LSEQ=CAATAATACGAGTAAGAACC;RSEQ=TTAATAAAGTGACTTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2443:1213:706,507:700,528:1228,1213:0.4965:2,2:38.4:1:34.4:1:0.56643:1.05:60:66.389:0.4938:0.0176:1.1 0/1:2521:1229:709,520:737,552:1289,1229:0.4875:2,2:38.6:1:34.4:1:0.80892:1.02:60:80.933:0.4856:0.0206:1.1
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chr3 142292296 142292296 A - intronic ATR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 247 432 chr3 142292295 . CA C 247 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=406;VD=119;AF=0.2931;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.13376;SOR=0.83815;LSEQ=GACAGAGTGAGACTTCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:119:94,25:126,23:149,119:0.2931:2,2:40.6:1:35:0:0.26371:1.45489:60:238:0.2946:0:0.2 0/1:432:143:115,28:121,30:151,143:0.331:2,2:37.7:1:34.6:1:1:1.02:60:142:0.3302:0.0509:0.2
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chr3 142292349 142292349 A - intronic ATR . . . . . . . . . . . . . . . . . . . . . 0.0050 0.0018 0.0377 0.0044 0 0.0481 0.0032 0.0092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q23 0.5 232 518 chr3 142292348 . TA T 232 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=570;VD=99;AF=0.1737;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11189;SOR=1.24128;LSEQ=ATGCTACTAAATAAAGTCCT;RSEQ=AAAAAAAAAAAGAATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:99:68,31:304,152:456,99:0.1737:2,2:41:1:35:1:0.72516:1.10:60:198:0.174:0.0158:0.2 0/1:518:75:47,28:272,158:430,75:0.1448:2,2:45.1:1:35:1:1:1.02555:60:150:0.1462:0.0077:0.3
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chr3 178922274 178922274 C A intron PIK3CA NM_006218:exon6:c.1060-17C>A . . rs2699896 ID=COSV55874930;OCCURENCE=1(breast),2(meninges),40(large_intestine),20(soft_tissue),1(upper_aerodigestive_tract) 251012 Cowden_syndrome|not_specified|not_provided MONDO:MONDO:0016063,MedGen:C0018553,OMIM:PS158350,Orphanet:ORPHA201,SNOMED_CT:58037000|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.584665 0.248 0.6697 0.5574 0.8631 0.4759 0.2550 0.4740 0.5801 0.5218 0.5598 0.6189 0.8533 0.5203 0.6689 0.2710 0.4851 0.5604 0.5509 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q26.32 1 351 1105 chr3 178922274 . C A 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1028;VD=1028;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51805;SOR=0;LSEQ=GTGTATACATTAGTATATAC;RSEQ=TACTTTTTTCTTTTAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1028:1028:724,304:0,0:0,1028:1:0,2:41.9:1:34.8:1:1:0:60:256:1:0.0039:1.3 1/1:1105:1104:789,315:0,0:0,1104:0.9991:0,2:39.2:1:34.8:1:1:0:60:551:1:0.0471:1.3
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chr3 178938747 178938747 A T intron PIK3CA NM_006218:exon14:c.2016-27A>T . . rs6443625 ID=COSV55887980;OCCURENCE=37(meninges),11(soft_tissue),1(lung) 1220873 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.272963 0.1091 0.2479 0.3027 0.4626 0.3247 0.2101 0.2288 0.2947 0.2939 0.2818 0.2446 0.4260 0.2279 0.3146 0.1066 0.1633 0.1770 0.1752 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q26.32 0.5 328 1408 chr3 178938747 . A T 328 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1308;VD=652;AF=0.4985;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.20988;SOR=1.06706;LSEQ=ATTTAAGACTATATATATAT;RSEQ=TTTTTAATTTTGCACGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1308:652:441,211:453,177:630,652:0.4985:2,2:42.7:1:35:1:0.10087:1.22433:60:1304:0.5062:0:1.1 0/1:1408:679:472,207:476,191:667,679:0.4822:2,2:41.7:1:34.9:1:0.47378:1.09288:60:678:0.5:0:1.1
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chr3 178942431 178942431 C G intronic PIK3CA . . . rs2699889 ID=COSV55874955;OCCURENCE=20(soft_tissue),1(upper_aerodigestive_tract),32(large_intestine) 1273148 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.629393 0.2679 . . . . . . . . . 0.6499 0.9127 0.5484 0.7119 0.2930 0.4939 0.5800 0.5724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3q26.32 1 347 1069 chr3 178942431 . C G 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1063;VD=1061;AF=0.9981;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68556;SOR=0.99438;LSEQ=TTATATTTTAAAATAAATTT;RSEQ=AGGGTAAAATAATAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1063:1061:779,282:0,0:0,1061:0.9981:0,2:39.1:1:34.4:1:1:0:60:65.312:0.9981:0.0292:1.1 1/1:1069:1067:777,290:0,0:0,1067:0.9981:0,2:38:1:34.5:1:1:0:60:132.375:0.9991:0.0281:1.1
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chr4 1801511 1801511 C T exonic FGFR3 . synonymous SNV FGFR3:NM_000142:exon4:c.417C>T:p.D139D,FGFR3:NM_001163213:exon4:c.417C>T:p.D139D,FGFR3:NM_001354809:exon4:c.417C>T:p.D139D,FGFR3:NM_001354810:exon4:c.417C>T:p.D139D,FGFR3:NM_022965:exon4:c.417C>T:p.D139D rs3135867 ID=COSV99600667;OCCURENCE=18(meninges) 251372 Craniosynostosis_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.0201677 . 0.0373 0.0385 0.0062 0.0165 0.0004 0.0534 0.0488 0.0627 0.0484 0.0367 0.0088 0.0347 0.0728 0.0006 0.0441 0.0539 0.0451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4p16.3 0.5 357 2473 chr4 1801511 . C T 357 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2542;VD=1259;AF=0.4953;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40009;SOR=1.01602;LSEQ=GATGACGAAGACGGGGAGGA;RSEQ=GAGGCTGAGGACACAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2542:1259:715,544:772,505:1277,1259:0.4953:2,2:39.1:1:34.7:1:0.06367:1.16303:60:313.75:0.4978:0.0142:1.1 0/1:2473:1215:760,455:735,521:1256,1215:0.4913:2,2:39.6:1:34.9:1:0.04371:1.18:60:1214:0.4935:0.015:1.2
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chr4 1807894 1807894 G A exonic FGFR3 . synonymous SNV FGFR3:NM_022965:exon12:c.1617G>A:p.T539T,FGFR3:NM_000142:exon14:c.1953G>A:p.T651T,FGFR3:NM_001163213:exon14:c.1959G>A:p.T653T,FGFR3:NM_001354809:exon14:c.1956G>A:p.T652T,FGFR3:NM_001354810:exon14:c.1956G>A:p.T652T rs7688609 ID=COSV99600161;OCCURENCE=18(meninges),3(central_nervous_system),2(biliary_tract),1(soft_tissue) 861287 Squamous_cell_lung_carcinoma|not_specified Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MedGen:CN169374 no_assertion_criteria_provided Benign/Likely_benign 0.95607 1 0.9551 0.9874 0.8618 0.9934 1 1 0.9996 0.9971 0.9999 0.9604 0.8608 0.9988 1 1 1 0.9997 0.9929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4p16.3 1 403 3061 chr4 1807894 . G A 403 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3008;VD=2998;AF=0.9967;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57277;SOR=0.98263;LSEQ=CTCGACTACTACAAGAAGAC;RSEQ=ACCAACGTGAGCCCGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3008:2998:1792,1206:0,1:1,2998:0.9967:0,2:38:1:34.9:1:0.40247:0:60:748.5:0.999:0.015:1.2 1/1:3061:3051:1755,1296:2,1:3,3051:0.9967:2,2:36.7:1:34.9:1:1:1.47674:60:1524.5:0.9977:0.0461:1.2
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chr4 55130078 55130078 T C exonic PDGFRA . synonymous SNV PDGFRA:NM_001347827:exon4:c.612T>C:p.N204N,PDGFRA:NM_001347829:exon4:c.612T>C:p.N204N,PDGFRA:NM_001347830:exon4:c.651T>C:p.N217N,PDGFRA:NM_006206:exon4:c.612T>C:p.N204N,PDGFRA:NM_001347828:exon5:c.687T>C:p.N229N rs2229307 ID=COSV57264195;OCCURENCE=2(meninges),3(large_intestine),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),6(soft_tissue) 251492 Gastrointestinal_stromal_tumor|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.236222 0.2034 0.1650 0.1853 0.2607 0.4372 0.1801 0.1240 0.1176 0.1676 0.2247 0.1677 0.2562 0.3759 0.07 0.1780 0.1216 0.1175 0.1487 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 339 1813 chr4 55130078 . T C 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1843;VD=908;AF=0.4927;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31094;SOR=0.96577;LSEQ=TTCCAGACCATCCCATTTAA;RSEQ=GTTTATGCTTTAAAAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1843:908:472,436:461,472:933,908:0.4927:2,2:37.5:1:34.3:1:0.28365:1.11:60:99.889:0.4907:0.0217:1.5 1/0:1813:909:434,475:440,463:903,909:0.5014:2,2:36.7:1:34.5:1:0.70685:1.0401:60:180.8:0.5008:0.0254:1.5
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chr4 55130154 55130154 G A intronic PDGFRA . . . rs2307049 ID=COSV99956052;OCCURENCE=3(central_nervous_system) 1268667 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.235623 0.2034 . 0.2149 0.2906 0.4716 0.2232 0.1336 0.1428 0.1898 0.2446 0.1681 0.2566 0.3756 0.0695 0.1778 0.1215 0.1178 0.1504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 311 929 chr4 55130154 . G A 311 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=989;VD=483;AF=0.4884;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47496;SOR=0.99014;LSEQ=CAGGCAAAATCATAAGGTGC;RSEQ=TGTAGGATTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:989:483:191,292:199,307:506,483:0.4884:2,2:37.9:1:34.9:1:0.94821:1.01:60:966:0.4959:0.0243:1.8 0/1:929:456:175,281:198,273:471,456:0.4909:2,2:40.5:1:34.8:1:0.28381:1.16439:60:455:0.4978:0.0151:1.8
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chr4 55133726 55133726 T G exonic PDGFRA . synonymous SNV PDGFRA:NM_001347827:exon7:c.939T>G:p.G313G,PDGFRA:NM_001347829:exon7:c.939T>G:p.G313G,PDGFRA:NM_001347830:exon7:c.978T>G:p.G326G,PDGFRA:NM_006206:exon7:c.939T>G:p.G313G,PDGFRA:NM_001347828:exon8:c.1014T>G:p.G338G rs4358459 ID=COSV57264201;OCCURENCE=1(oesophagus),2(meninges),3(large_intestine),4(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),6(soft_tissue) 251493 Gastrointestinal_stromal_tumor|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.234225 0.2034 0.1632 0.1837 0.2566 0.4345 0.1795 0.1245 0.1157 0.1671 0.2239 0.1669 0.2557 0.3747 0.0662 0.1782 0.1219 0.1162 0.1472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 356 2704 chr4 55133726 . T G 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2779;VD=1339;AF=0.4818;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18194;SOR=0.95076;LSEQ=CTTCCCTGTACAGAGAAAGG;RSEQ=TTCATTGAAATCAAACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2779:1339:762,577:781,653:1434,1339:0.4818:2,2:38:1:34.3:1:0.2069:1.10:60:77.765:0.4807:0.0097:1.1 0/1:2704:1337:774,563:770,594:1364,1337:0.4945:2,2:37.8:1:33.9:1:0.46012:1.06:60:45.103:0.4906:0.0174:1.1
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chr4 55139771 55139771 T C exonic PDGFRA . nonsynonymous SNV PDGFRA:NM_001347827:exon10:c.1432T>C:p.S478P,PDGFRA:NM_001347829:exon10:c.1432T>C:p.S478P,PDGFRA:NM_001347830:exon10:c.1471T>C:p.S491P,PDGFRA:NM_006206:exon10:c.1432T>C:p.S478P,PDGFRA:NM_001347828:exon11:c.1507T>C:p.S503P rs35597368 ID=COSV57266881;OCCURENCE=5(soft_tissue),2(meninges),2(large_intestine),3(central_nervous_system) 50233 Gastrointestinal_stromal_tumor|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.199281 0.1706 0.1443 0.1566 0.2340 0.3021 0.1444 0.1231 0.1038 0.1614 0.2085 0.1473 0.2301 0.2596 0.0497 0.1338 0.1224 0.1024 0.1424 0.305 0.142 T 0.234 0.035 N 1 0.090 P -0.345 0.033 N -0.95 0.754 T -0.16 0.095 N -1.098 0.043 T 0.000 0.000 T . . . . . 0.007 0.030 N c -1.510 -1.466 1.000 0.409 0.447 0.083 0 0.811 0.178 -1.151 0.033 -0.364 0.068 0.000 0.063 0.000 0.016 6.025 0.188 Immunoglobulin-like fold . . 4q12 0.5 355 2691 chr4 55139771 . T C 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2594;VD=1289;AF=0.4969;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17093;SOR=1.05528;LSEQ=ACATCATCACGGAGATCCAC;RSEQ=CCCGAGACAGGAGTACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2594:1289:752,537:727,571:1298,1289:0.4969:2,2:39.2:1:34.6:1:0.23353:1.10:60:183.143:0.4971:0.005:1.1 0/1:2691:1301:752,549:793,593:1386,1301:0.4835:2,2:37.6:1:34.4:1:0.78463:1.02:60:117.273:0.4824:0.0201:1.1
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chr4 55141055 55141055 A G exonic PDGFRA . synonymous SNV PDGFRA:NM_001347827:exon12:c.1701A>G:p.P567P,PDGFRA:NM_001347829:exon12:c.1701A>G:p.P567P,PDGFRA:NM_001347830:exon12:c.1740A>G:p.P580P,PDGFRA:NM_006206:exon12:c.1701A>G:p.P567P,PDGFRA:NM_001347828:exon13:c.1776A>G:p.P592P rs1873778 ID=COSV99955338;OCCURENCE=2(liver),18(meninges),3(central_nervous_system),2(biliary_tract),1(soft_tissue) 251495 Squamous_cell_lung_carcinoma|Gastrointestinal_stromal_tumor|Carcinoma_of_colon|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.957668 1 0.9589 0.9881 0.8816 0.9919 1 0.9998 0.9984 0.9942 0.9996 0.9677 0.8906 0.9881 0.9834 0.9994 1 0.9986 0.9908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 1 389 2472 chr4 55141055 . A G 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2418;VD=2396;AF=0.9909;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47084;SOR=0.93317;LSEQ=GTCATTGAATCAATCAGCCC;RSEQ=GATGGACATGAATATATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2418:2396:1388,1008:1,2:3,2396:0.9909:2,2:39.3:1:34.6:1:0.57637:2.75:60:132.111:0.9975:0.0182:1.1 1/1:2472:2451:1359,1092:4,4:8,2451:0.9915:2,2:38.6:1:34.6:1:1:1.24:60:152.188:0.9947:0.0344:1.1
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chr4 55143577 55143577 G A exonic PDGFRA . synonymous SNV PDGFRA:NM_001347827:exon13:c.1809G>A:p.A603A,PDGFRA:NM_001347829:exon13:c.1809G>A:p.A603A,PDGFRA:NM_001347830:exon13:c.1848G>A:p.A616A,PDGFRA:NM_006206:exon13:c.1809G>A:p.A603A,PDGFRA:NM_001347828:exon14:c.1884G>A:p.A628A rs10028020 ID=COSV57265177;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),5(soft_tissue),1(skin),2(meninges),2(large_intestine),3(central_nervous_system) 251496 Gastrointestinal_stromal_tumor|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.228035 0.1726 0.1662 0.1636 0.3138 0.3214 0.1475 0.1128 0.0999 0.1614 0.2118 0.1664 0.3054 0.2763 0.0497 0.1379 0.1125 0.0999 0.1337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 327 1424 chr4 55143577 . G A 327 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1438;VD=682;AF=0.4743;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42001;SOR=1.01808;LSEQ=CGGGTCTTGGGGTCTGGAGC;RSEQ=TTTGGGAAGGTGGTTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1438:682:420,262:488,263:751,682:0.4743:2,2:40.2:1:34.8:1:0.18802:1.15737:60:681:0.4746:0.0076:1.1 0/1:1424:669:460,209:483,270:753,669:0.4698:2,2:39.7:1:34.8:1:0.07206:1.23:60:668:0.4708:0.0098:1.1
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chr4 55151958 55151958 - A intron PDGFRA NM_001347828:exon19:c.2515-50->A;NM_006206:exon18:c.2440-50->A;NM_001347829:exon18:c.2440-50->A;NM_001347830:exon18:c.2479-50->A . . rs3830355 ID=COSV99955341;OCCURENCE=10(meninges) 861306 Squamous_cell_lung_carcinoma|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.713858 0.8224 0.7497 0.8001 0.5254 0.6617 0.8481 0.8730 0.8641 0.8213 0.7813 0.7650 0.5355 0.6850 0.9362 0.8600 0.8726 0.8597 0.8279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 352 2283 chr4 55151958 . T TA 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=2268;VD=1058;AF=0.4665;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12429;SOR=0.93216;LSEQ=GTCTTGCAGGGGTGATGCTA;RSEQ=TCAGCTACAGATGGCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2268:1058:753,305:812,392:1204,1058:0.4665:2,2:40.9:1:35:1:0.05549:1.19:60:2116:0.8817:0.0507:0.1 0/1:2283:1105:769,336:830,344:1174,1105:0.484:2,2:40.9:1:34.9:1:0.58265:1.05417:60:2210:0.9436:0.046:0.1
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chr4 55152040 55152040 C T exonic PDGFRA . synonymous SNV PDGFRA:NM_001347829:exon18:c.2472C>T:p.V824V,PDGFRA:NM_001347830:exon18:c.2511C>T:p.V837V,PDGFRA:NM_006206:exon18:c.2472C>T:p.V824V,PDGFRA:NM_001347828:exon19:c.2547C>T:p.V849V rs2228230 ID=COSV57264143;OCCURENCE=2(breast),4(meninges),2(large_intestine),6(central_nervous_system),2(biliary_tract),12(haematopoietic_and_lymphoid_tissue),1(urinary_tract),17(soft_tissue),2(skin),1(endometrium) 251497 Gastrointestinal_stromal_tumor|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.240415 0.1726 0.1983 0.1857 0.3310 0.3309 0.1415 0.1275 0.1352 0.1729 0.2184 0.1941 0.3254 0.3026 0.0633 0.1316 0.1271 0.1392 0.1582 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 365 2932 chr4 55152040 . C T 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2892;VD=1470;AF=0.5083;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42439;SOR=1.01143;LSEQ=GATCTGGCTGCTCGCAACGT;RSEQ=CTCCTGGCACAAGGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2892:1470:837,633:824,591:1415,1470:0.5083:2,2:38:1:34.7:1:0.4977:1.05438:60:209:0.5106:0.0149:1.1 1/0:2932:1482:810,672:839,600:1439,1482:0.5055:2,2:38.1:1:34.7:1:0.04799:1.16004:60:133.727:0.5081:0.0208:1.1
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chr4 55161254 55161254 C T intron PDGFRA NM_001347828:exon24:c.3198-38C>T;NM_006206:exon23:c.3123-38C>T;NM_001347829:exon23:c.3123-38C>T;NM_001347830:exon23:c.3162-38C>T . . rs3733540 ID=COSV99955593;OCCURENCE=2(meninges) 251498 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.699081 0.8274 0.7358 0.7981 0.4766 0.6586 0.8577 0.8735 0.8671 0.8242 0.7821 0.7539 0.4871 0.6802 0.9205 0.8671 0.8726 0.8649 0.8262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 342 1975 chr4 55161254 . C T 342 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1982;VD=937;AF=0.4728;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.44532;SOR=0.98928;LSEQ=AGTCTAGGTCTAGTTCTGTG;RSEQ=AGGAGTTGTAATATTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1982:937:629,308:674,369:1043,937:0.4728:2,2:39.8:1:34.8:1:0.25486:1.12:60:467.5:0.4744:0.0207:1.2 0/1:1975:939:645,294:709,325:1034,939:0.4754:2,2:39.7:1:34.7:1:0.96129:1.01:60:312:0.4773:0.0238:1.2
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chr4 55161391 55161391 T C exonic PDGFRA . synonymous SNV PDGFRA:NM_001347829:exon23:c.3222T>C:p.D1074D,PDGFRA:NM_001347830:exon23:c.3261T>C:p.D1087D,PDGFRA:NM_006206:exon23:c.3222T>C:p.D1074D,PDGFRA:NM_001347828:exon24:c.3297T>C:p.D1099D rs7685117 ID=COSV99955343;OCCURENCE=18(meninges),3(central_nervous_system) 251499 Gastrointestinal_stromal_tumor|Idiopathic_hypereosinophilic_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0011895,MedGen:C0206141,OMIM:607685,Orphanet:ORPHA3260,SNOMED_CT:423294001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.997204 1 0.9968 0.9991 0.9905 0.9998 1 1 1.0000 1 0.9995 0.9980 0.9929 1 1 1 1 1 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 1 389 2497 chr4 55161391 . T C 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2516;VD=2506;AF=0.996;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.20609;SOR=1.51437;LSEQ=GAAGACATCGACATGATGGA;RSEQ=GACATCGGCATAGACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2516:2506:1371,1135:0,2:2,2506:0.996:0,2:39.3:1:34.5:1:0.20543:0:60:99.24:0.9976:0.0429:1.3 1/1:2497:2482:1394,1088:2,1:3,2482:0.994:2,2:40.5:1:34.5:1:1:1.5607:60:123.1:0.996:0.0272:1.3
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chr4 55524252 55524252 G A intron KIT NM_001093772:exon1:c.67+4G>A;NM_000222:exon1:c.67+4G>A . . rs72550820 ID=COSV55390550;OCCURENCE=1(soft_tissue) 221464 Partial_albinism|Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0001044,Human_Phenotype_Ontology:HP:0007443,Human_Phenotype_Ontology:HP:0007544,MONDO:MONDO:0008244,MedGen:C0080024,OMIM:172800,Orphanet:ORPHA2884,SNOMED_CT:6479008|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.00938498 . 0.0128 0.0121 0.0031 0.0047 0 0.0064 0.0146 0.0119 0.0214 0.0097 0.0020 0.0084 0.0033 0.0006 0.0063 0.0159 0.0132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 337 1825 chr4 55524252 . G A 337 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1749;VD=872;AF=0.4986;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19839;SOR=1.0607;LSEQ=GCTTCGCGTCCAGACAGGTG;RSEQ=GACACCGCGGCTGGCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1749:872:401,471:423,450:873,872:0.4986:2,2:39.9:1:34.4:1:0.31407:1.10403:60:108:0.4991:0.0154:1.2 0/1:1825:883:400,483:452,483:935,883:0.4838:2,2:41.2:1:34.5:1:0.20432:1.12992:60:97.111:0.4847:0.0214:1.1
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chr4 55569859 55569859 - T intron KIT NM_001093772:exon5:c.757-31->T;NM_000222:exon5:c.757-31->T . . rs544780604 ID=COSV55415315;OCCURENCE=1(stomach) . . . . . 0.000599042 0.001 0.0037 0.0009 0.0005 0.0012 0.0015 0 0.0010 0.0017 0.0007 3.26e-05 0 0 0 0 0 6.71e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 190 1581 chr4 55569859 . A AT 190 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1484;VD=37;AF=0.0249;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.2752;SOR=0.85331;LSEQ=TAAATTATATGGTAATCTTC;RSEQ=TTTTTTTTTCTCCTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1484:37:27,10:925,372:1297,37:0.0249:2,2:46.2:1:35:0:1:1.09:60:74:0.0288:0:0.2 0/1:1581:46:29,16:1016,362:1378,46:0.0291:2,2:34.6:1:34.5:1:0.17178:1.54797:60:92:0.0334:0.0044:0.1
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chr4 55602765 55602765 G C exonic KIT . synonymous SNV KIT:NM_000222:exon18:c.2586G>C:p.L862L,KIT:NM_001093772:exon18:c.2574G>C:p.L858L rs3733542 ID=COSV55388515;OCCURENCE=3(meninges),1(large_intestine),2(bone),1(stomach),6(haematopoietic_and_lymphoid_tissue),4(soft_tissue) 251505 Partial_albinism|Mastocytosis|Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0001044,Human_Phenotype_Ontology:HP:0007443,Human_Phenotype_Ontology:HP:0007544,MONDO:MONDO:0008244,MedGen:C0080024,OMIM:172800,Orphanet:ORPHA2884,SNOMED_CT:6479008|Human_Phenotype_Ontology:HP:0100495,MONDO:MONDO:0007950,MedGen:C0024899,Orphanet:ORPHA98292|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.164137 0.0565 0.1931 0.1147 0.3398 0.0538 0.0480 0.0527 0.1095 0.0925 0.1068 0.1561 0.3272 0.0935 0.0960 0.0464 0.0518 0.1006 0.1079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 337 1808 chr4 55602765 . G C 337 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1753;VD=817;AF=0.4661;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01009;SOR=0.8538;LSEQ=GGGATTTTTCTTTGGGAGCT;RSEQ=TTCTCTTTAGGTAAAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1753:817:486,331:542,391:933,817:0.4661:2,2:38.3:1:34.3:1:0.5596:1.06:60:67.083:0.4653:0.0194:1.1 1/0:1808:914:548,366:525,366:891,914:0.5055:2,2:39.1:1:34.3:1:0.66629:1.04:60:82.091:0.5039:0.0243:1.1
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chr4 55948108 55948108 A G intron KDR NM_002253:exon29:c.3848+15T>C . . rs2412617 ID=COSV99817104;OCCURENCE=3(central_nervous_system) 508794 Hemangioma,_capillary_infantile|not_specified MONDO:MONDO:0011191,MedGen:C1865871,OMIM:602089|MedGen:CN169374 no_assertion_criteria_provided Benign 0.996805 1 0.9976 0.9986 0.9922 0.9968 1 1 0.9992 0.9971 1 0.9975 0.9923 1 0.9967 1 1 0.9995 0.9980 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 1 354 1120 chr4 55948108 . A G 354 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1232;VD=1222;AF=0.9919;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19791;SOR=0.54812;LSEQ=TTGAAATTTGTCTTTTTAAT;RSEQ=TGGCTGAGTCTTACCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1232:1222:824,398:0,0:0,1222:0.9919:0,2:38.5:1:34.6:1:1:0:60:202.667:0.9918:0.0341:1.1 1/1:1120:1115:749,366:0,0:0,1115:0.9955:0,2:39.2:1:34.6:1:1:0:60:122.889:0.9973:0.0348:1.1
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chr4 55968044 55968044 T - intron KDR NM_002253:exon15:c.2266+20A>- . . rs779577525 ID=COSV55761838;OCCURENCE=1(breast),3(large_intestine),1(stomach) . . . . . . . . 0.0006 0.0004 0.0010 0.0003 0.0008 0.0006 0.0015 0.0003 9.839e-05 0.0001 0 0 0.0013 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 190 1684 chr4 55968043 . AT A 190 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1670;VD=42;AF=0.0251;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.47217;SOR=0.96158;LSEQ=CCATGGTGTATATGTACCAC;RSEQ=TTTTTTTTATCCCACTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1670:42:29,13:1074,553:1627,42:0.0251:2,2:35.3:1:35:1:0.74374:1.15:60:84:0.0252:0.0024:0.4 0/1:1684:44:29,15:1106,533:1639,44:0.0261:2,2:38:1:34.9:1:0.8708:1.07325:60:88:0.0262:0.0053:0.5
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chr4 55968053 55968053 A C intron KDR NM_002253:exon15:c.2266+11T>G . . rs7655964 ID=COSV55758590;OCCURENCE=8(meninges),3(central_nervous_system),15(soft_tissue),1(lung) . . . . . 0.292931 0.3135 0.2826 0.3486 0.1485 0.5786 0.3249 0.3752 0.3460 0.3545 0.3108 0.3084 0.1496 0.5298 0.2947 0.3079 0.3853 0.3656 0.3864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q12 0.5 330 1823 chr4 55968053 . A C 330 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1810;VD=900;AF=0.4972;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21893;SOR=1.05513;LSEQ=TATGTACCACATTTTTTTTT;RSEQ=TCCCACTGACCTTCTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1810:900:592,308:603,302:905,900:0.4972:2,2:38.1:1:33.7:1:0.72764:1.03881:60:41.857:0.5014:0.0182:1.1 0/1:1823:882:598,284:627,312:939,882:0.4838:2,2:37.3:1:34.4:1:0.65313:1.05:60:109.25:0.4853:0.0263:1.1
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chr4 153252061 153252061 A G intron FBXW7 NM_001349798:exon9:c.986-41T>C;NM_001013415:exon6:c.632-41T>C;NM_018315:exon6:c.746-41T>C;NM_033632:exon7:c.986-41T>C . . rs10033601 ID=COSV55895919;OCCURENCE=3(central_nervous_system),12(soft_tissue),1(upper_aerodigestive_tract) 1249237 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.48123 0.4484 0.4141 0.3783 0.6639 0.4535 0.4490 0.3470 0.3051 0.3546 0.3912 0.4135 0.6600 0.4412 0.4172 0.4531 0.3262 0.2892 0.3436 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q31.3 0.5 332 1539 chr4 153252061 . A G 332 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1619;VD=790;AF=0.488;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49911;SOR=0.99731;LSEQ=AGTAAATTGCCTTCACCAAT;RSEQ=ATAACAGTTATACATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1619:790:308,482:339,489:828,790:0.488:2,2:43.4:1:34.5:1:0.44643:1.08484:60:196.5:0.487:0.0111:1.1 0/1:1539:752:280,472:327,457:784,752:0.4886:2,2:43.1:1:34.5:1:0.07605:1.20604:60:93:0.4869:0.0156:1.1
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chr4 153268228 153268228 A - intron FBXW7 NM_001349798:exon6:c.585-5T>-;NM_001013415:exon3:c.231-5T>-;NM_018315:exon3:c.345-5T>-;NM_033632:exon4:c.585-5T>- . . rs780809685 ID=COSV55891341;OCCURENCE=4(skin),1(upper_aerodigestive_tract) . . . . . . . . 0.3634 0.3337 0.3654 0.3399 0.3661 0.3670 0.3629 0.3751 0.0382 0.0066 0.0974 0.1 0 0.1705 0.0424 0.0641 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q31.3 0.5 281 1387 chr4 153268227 . CA C 281 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1432;VD=262;AF=0.183;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.2741;SOR=0.93938;LSEQ=GTACAAGCCCAGTGGTACTA;RSEQ=AAAAAAAAAAAAAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1432:262:128,134:525,509:1034,262:0.183:2,2:46.8:1:34.9:1:0.58094:1.07971:60:524:0.1835:0.0035:0.2 0/1:1387:267:142,125:569,449:1018,267:0.1925:2,2:48.2:1:34.9:1:0.44714:1.11545:60:534:0.1935:0.0058:0.3
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chr4 153268240 153268240 A G intron FBXW7 NM_001349798:exon6:c.585-17T>C;NM_001013415:exon3:c.231-17T>C;NM_018315:exon3:c.345-17T>C;NM_033632:exon4:c.585-17T>C . . rs1021717666 ID=COSV55956380;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(stomach) . . . . . . . . 0.0002 0.0001 0 0.0004 0 4.118e-05 0 0.0006 9.824e-05 0.0003 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q31.3 0.25 140 1220 chr4 153268240 . A G 140 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=SNV;DP=1262;VD=11;AF=0.0087;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.14905;SOR=0.62235;LSEQ=GGTACTACAAAAAAAAAAAA;RSEQ=AGAGAGAGAGAAAGGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1262:11:7,4:560,603:1163,11:0.0087:2,2:22.1:1:26.5:1:0.3719:1.88:60:2.667:0.0068:0:1.1 0/1:1220:17:8,9:609,513:1122,17:0.0139:2,2:21.2:1:34.4:1:0.62773:1.33518:60:34:0.015:0:1.2
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chr4 153332605 153332607 CTC - exonic FBXW7 . nonframeshift deletion FBXW7:NM_033632:exon2:c.349_351del:p.E117del,FBXW7:NM_001257069:exon4:c.349_351del:p.E117del,FBXW7:NM_001349798:exon4:c.349_351del:p.E117del rs781154022 ID=COSV55908674;OCCURENCE=2(breast),1(bone),2(haematopoietic_and_lymphoid_tissue),2(kidney) . . . . . . . 0.0002 0.0006 0.0003 0.0005 0 0.0002 0.0006 0 0.0014 9.716e-05 0 0 0 0 0 0.0002 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4q31.3 0.5 171 2285 chr4 153332604 . TCTC T 171 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2348;VD=30;AF=0.0128;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.5093;SOR=0.97282;LSEQ=ATCGTCACTCTCCTGGTCCA;RSEQ=CTCCTCCTCCTCATCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2348:30:20,10:1190,1126:2316,30:0.0128:2,2:32.4:1:34.6:1:0.1016:1.89:60:60:0.013:0.0017:0.1 0/1:2285:30:22,8:1172,1082:2254,30:0.0131:2,2:37.1:1:35:1:0.0259:2.54:60:60:0.0133:0.0009:0.1
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chr5 228278 228278 - T intron SDHA NM_001330758:exon6:c.622-22->T;NM_001294332:exon5:c.478-22->T;NM_004168:exon6:c.622-22->T . . rs200467868 . . . . . . 0.00119808 0.006 . 0.0006 0 0.0005 0.0051 0 0.0003 0 6.241e-05 0.0005 0 0 0 0.0093 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5p15.33 0.5 198 1674 chr5 228278 . C CT 198 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1723;VD=38;AF=0.0221;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.07667;SOR=0.71776;LSEQ=TTGGCTTAACACTTCTTGCC;RSEQ=TTTTTTTTTCCTTTCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1723:38:29,9:967,540:1507,38:0.0221:2,2:40.1:1:35:1:0.16869:1.80:60:76:0.0259:0.0017:0.1 0/1:1674:51:32,18:943,513:1456,51:0.0305:2,2:42.9:1:35:0:0.88176:1.034:59:102:0.0356:0:0.1
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chr5 230980 230980 A G intron SDHA NM_001330758:exon7:c.771-11A>G;NM_001294332:exon6:c.627-11A>G;NM_004168:exon7:c.771-11A>G . . rs2288461 ID=COSV53768388;OCCURENCE=1(breast) 251940 Leigh_syndrome|Dilated_cardiomyopathy_1GG|Hereditary_cancer-predisposing_syndrome|Hereditary_Paraganglioma-Pheochromocytoma_Syndromes|Neurodegeneration_with_ataxia_and_late-onset_optic_atrophy|Mitochondrial_complex_II_deficiency,_nuclear_type_1|not_specified|not_provided MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0013339,MedGen:C3150898,OMIM:613642|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072|MONDO:MONDO:0031006,MedGen:C5543254,OMIM:619259|MONDO:MONDO:0100294,MedGen:C1855008,OMIM:252011,Orphanet:ORPHA3208|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.858427 0.628 0.9126 0.8826 0.9753 0.8946 0.6711 0.9190 0.8853 0.8746 0.9007 0.9009 0.9713 0.8923 0.7848 0.6590 0.9201 0.8853 0.8867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5p15.33 1 389 2290 chr5 230980 . A G 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2378;VD=2371;AF=0.9971;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57697;SOR=1.03855;LSEQ=GTGTGCAGTCACTGCTCTCT;RSEQ=TTGTTTCCAGAGGCTACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2378:2371:1514,857:2,0:2,2371:0.9971:0,2:39.7:1:34.7:1:0.53837:0:60:236.1:0.9987:0.0336:1.3 1/1:2290:2283:1440,843:2,0:2,2283:0.9969:0,2:39.8:1:34.6:1:0.53416:0:60:325.143:0.9978:0.0336:1.3
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chr5 231111 231111 T C exonic SDHA . synonymous SNV SDHA:NM_001294332:exon6:c.747T>C:p.P249P,SDHA:NM_001330758:exon7:c.891T>C:p.P297P,SDHA:NM_004168:exon7:c.891T>C:p.P297P rs1126417 ID=COSV53767683;OCCURENCE=1(liver),1(lung),1(thyroid) 135730 Leigh_syndrome|Dilated_cardiomyopathy_1GG|Paragangliomas_5|Hereditary_cancer-predisposing_syndrome|Hereditary_Paraganglioma-Pheochromocytoma_Syndromes|Neurodegeneration_with_ataxia_and_late-onset_optic_atrophy|Mitochondrial_complex_II_deficiency,_nuclear_type_1|not_specified|not_provided MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0013339,MedGen:C3150898,OMIM:613642|MONDO:MONDO:0013602,MedGen:C3279992,OMIM:614165|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072|MONDO:MONDO:0031006,MedGen:C5543254,OMIM:619259|MONDO:MONDO:0100294,MedGen:C1855008,OMIM:252011,Orphanet:ORPHA3208|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.653355 0.3363 0.7687 0.7045 0.7853 0.6446 0.3271 0.7652 0.7582 0.6844 0.6799 0.7402 0.7825 0.6516 0.7067 0.3323 0.7666 0.7589 0.7423 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5p15.33 1 384 2168 chr5 231111 . T C 384 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2166;VD=2147;AF=0.9912;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18694;SOR=0.68173;LSEQ=GAGTTTGTTCAGTTCCACCC;RSEQ=ACAGGTAGGGCAGGACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2166:2147:1017,1130:0,0:0,2147:0.9912:0,2:39.1:1:34.6:1:1:0:60:164.154:0.9944:0.03:1.2 1/1:2168:2155:964,1191:0,0:0,2155:0.994:0,2:38.3:1:34.7:1:1:0:60:238.444:0.9954:0.053:1.2
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chr5 1295243 1295243 G A upstream TERT dist=60 . . rs35550267 . 1327735 not_specified MedGen:CN169374 criteria_provided,_single_submitter Uncertain_significance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5p15.33 0.5 334 1870 chr5 1295243 . G A 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2118;VD=1098;AF=0.5184;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07131;SOR=1.09972;LSEQ=CCGGAGGGGGCTGGGCCGGG;RSEQ=ACCCGGGAGGGGTCGGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2118:1098:581,517:497,500:997,1098:0.5184:2,2:38.9:1:33.1:1:0.16173:1.13:60:22.87:0.5177:0.0118:1.2 0/1:1870:925:491,434:518,426:944,925:0.4947:2,2:39:1:33.4:1:0.45777:1.07476:60:36:0.4913:0.0155:1.2
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chr5 7870973 7870973 A G exonic MTRR . nonsynonymous SNV MTRR:NM_001364440:exon2:c.66A>G:p.I22M,MTRR:NM_001364441:exon2:c.66A>G:p.I22M,MTRR:NM_001364442:exon2:c.66A>G:p.I22M,MTRR:NM_002454:exon2:c.66A>G:p.I22M,MTRR:NM_024010:exon2:c.66A>G:p.I22M rs1801394 ID=COSV52943975;OCCURENCE=1(urinary_tract),2(pancreas),2(lung) 22068 Down_syndrome,_susceptibility_to|Neural_tube_defects,_folate-sensitive,_susceptibility_to|Gastrointestinal_stromal_tumor|Homocystinuria-Megaloblastic_anemia_due_to_defect_in_cobalamin_metabolism,_cblE_complementation_type|Disorders_of_Intracellular_Cobalamin_Metabolism|not_specified .|.|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0009354,MedGen:C1856057,OMIM:236270,Orphanet:ORPHA2169|MedGen:CN043592|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.364217 0.2629 0.4524 0.4694 0.2762 0.2222 0.2818 0.5779 0.5500 0.5101 0.5223 0.4607 0.2831 0.2823 0.4702 0.2784 0.5655 0.5647 0.5256 0.002 0.721 D 0.000 0.629 D 0.997 0.232 P 2.29 0.655 M -1.04 0.766 T -2.22 0.593 N -0.905 0.474 T 0.000 0.000 T . . . . . 0.105 0.158 N c -0.070 -0.272 1.000 0.458 0.737 0.974 0 0.334 0.151 0.098 0.149 1.199 0.960 0.012 0.185 0.996 0.625 8.87 0.343 Flavodoxin/nitric oxide synthase|Flavoprotein-like domain;Flavoprotein-like domain ENSG00000124275.10|ENSG00000124275.10|ENSG00000124275.10|ENSG00000124275.10|ENSG00000124275.10|ENSG00000124275.10|ENSG00000124275.10 Brain_Caudate_basal_ganglia|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Putamen_basal_ganglia|Cells_EBV-transformed_lymphocytes|Esophagus_Muscularis|Whole_Blood 5p15.31 0.5 335 1591 chr5 7870973 . A G 335 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1641;VD=797;AF=0.4857;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19263;SOR=0.93842;LSEQ=AAGGCCATCGCAGAAGAAAT;RSEQ=TGTGAGCAAGCTGTGGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1641:797:461,336:482,356:838,797:0.4857:2,2:39.7:1:34.7:1:0.92025:1.01:60:198.25:0.4853:0.0091:1.1 1/0:1591:798:429,369:459,332:791,798:0.5016:2,2:39.9:1:34.8:1:0.09542:1.18903:60:398:0.5013:0.0094:1.1
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chr5 112162854 112162854 T C exonic APC . synonymous SNV APC:NM_001127511:exon10:c.1404T>C:p.Y468Y,APC:NM_001354897:exon11:c.1488T>C:p.Y496Y,APC:NM_001354899:exon11:c.1374T>C:p.Y458Y,APC:NM_001354901:exon11:c.1281T>C:p.Y427Y,APC:NM_001354902:exon11:c.1185T>C:p.Y395Y,APC:NM_001354905:exon11:c.978T>C:p.Y326Y,APC:NM_000038:exon12:c.1458T>C:p.Y486Y,APC:NM_001354895:exon12:c.1458T>C:p.Y486Y,APC:NM_001354898:exon12:c.1383T>C:p.Y461Y,APC:NM_001354900:exon12:c.1335T>C:p.Y445Y,APC:NM_001354903:exon12:c.1155T>C:p.Y385Y,APC:NM_001354904:exon12:c.1080T>C:p.Y360Y,APC:NM_001127510:exon13:c.1458T>C:p.Y486Y,APC:NM_001354896:exon13:c.1512T>C:p.Y504Y,APC:NM_001354906:exon13:c.609T>C:p.Y203Y rs2229992 ID=COSV57321592;OCCURENCE=4(lung),1(thyroid),121(meninges),41(large_intestine),3(central_nervous_system) 51408 Hepatocellular_carcinoma|Neoplasm_of_stomach|Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|Desmoid_disease,_hereditary|not_specified|APC-Associated_Polyposis_Disorders|not_provided Human_Phenotype_Ontology:HP:0001402,Human_Phenotype_Ontology:HP:0002899,Human_Phenotype_Ontology:HP:0003007,Human_Phenotype_Ontology:HP:0006750,MONDO:MONDO:0007256,MedGen:C2239176,OMIM:114550,Orphanet:ORPHA88673,SNOMED_CT:187769009,SNOMED_CT:25370001|Human_Phenotype_Ontology:HP:0006753,MONDO:MONDO:0021085,MedGen:C0038356,SNOMED_CT:126824007|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:C1851124,OMIM:135290|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.509984 0.6647 0.4622 0.5796 0.2002 0.7183 0.6833 0.5059 0.5900 0.5766 0.6409 0.4692 0.2085 0.6579 0.5894 0.6538 0.5003 0.5762 0.5430 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 351 2336 chr5 112162854 . T C 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2224;VD=1104;AF=0.4964;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30777;SOR=0.96897;LSEQ=CAAGTGGACTGTGAAATGTA;RSEQ=GGGCTTACTAATGACCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2224:1104:657,447:618,496:1114,1104:0.4964:2,2:38.5:1:34.1:1:0.05877:1.18:60:72.6:0.4934:0.022:1.1 1/0:2336:1178:658,520:651,499:1150,1178:0.5043:2,2:38.8:1:34.5:1:0.73822:1.031:60:129.889:0.5032:0.021:1.1
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chr5 112164561 112164561 G A exonic APC . synonymous SNV APC:NM_001127511:exon12:c.1581G>A:p.A527A,APC:NM_001354897:exon13:c.1665G>A:p.A555A,APC:NM_001354899:exon13:c.1551G>A:p.A517A,APC:NM_001354901:exon13:c.1458G>A:p.A486A,APC:NM_001354902:exon13:c.1362G>A:p.A454A,APC:NM_001354905:exon13:c.1155G>A:p.A385A,APC:NM_000038:exon14:c.1635G>A:p.A545A,APC:NM_001354895:exon14:c.1635G>A:p.A545A,APC:NM_001354898:exon14:c.1560G>A:p.A520A,APC:NM_001354900:exon14:c.1512G>A:p.A504A,APC:NM_001354903:exon14:c.1332G>A:p.A444A,APC:NM_001354904:exon14:c.1257G>A:p.A419A,APC:NM_001127510:exon15:c.1635G>A:p.A545A,APC:NM_001354896:exon15:c.1689G>A:p.A563A,APC:NM_001354906:exon15:c.786G>A:p.A262A rs351771 ID=COSV57321606;OCCURENCE=3(lung),14(meninges),38(large_intestine),3(central_nervous_system) 51409 Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|not_specified|APC-Associated_Polyposis_Disorders|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.666134 0.8165 0.5864 0.6511 0.5316 0.7496 0.8236 0.5574 0.6168 0.6297 0.7194 0.5927 0.5342 0.6926 0.5894 0.8064 0.5564 0.6048 0.6212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 314 1162 chr5 112164561 . G A 314 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1127;VD=503;AF=0.4463;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39214;SOR=1.02693;LSEQ=ATTAATTTGCAGGTTATTGC;RSEQ=AGTGTTTTGAGGAATTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1127:503:357,146:424,199:623,503:0.4463:2,2:42.1:1:34.9:1:0.29886:1.15:60:250.5:0.4526:0.0133:1.1 0/1:1162:511:370,141:463,186:649,511:0.4398:2,2:40.3:1:34.9:1:0.69393:1.05:60:1022:0.4447:0.0275:1.1
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chr5 112171270 112171270 T - intronic APC . . . rs34632472 . . . . . . 0.496805 0.6548 . . . . . . . . . 0.3880 0.2524 0.5370 0.4474 0.6140 0.3683 0.4391 0.4021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 253 482 chr5 112171269 . AT A 253 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=441;VD=132;AF=0.2993;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.32441;SOR=0.92753;LSEQ=TCTTAGTATCCATAATAATA;RSEQ=TTTTTTTTTTTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:132:54,78:96,111:207,132:0.2993:2,2:49.2:1:35:1:0.36986:1.24842:60:264:0.3007:0.0045:0.1 0/1:482:152:68,84:118,119:237,152:0.3154:2,2:48.4:1:35:1:0.35032:1.22427:60:304:0.3167:0.0062:0.1
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chr5 112175770 112175770 G A exonic APC . synonymous SNV APC:NM_001127511:exon14:c.4425G>A:p.T1475T,APC:NM_001354897:exon15:c.4509G>A:p.T1503T,APC:NM_001354899:exon15:c.4395G>A:p.T1465T,APC:NM_001354901:exon15:c.4302G>A:p.T1434T,APC:NM_001354902:exon15:c.4206G>A:p.T1402T,APC:NM_001354905:exon15:c.3999G>A:p.T1333T,APC:NM_000038:exon16:c.4479G>A:p.T1493T,APC:NM_001354895:exon16:c.4479G>A:p.T1493T,APC:NM_001354898:exon16:c.4404G>A:p.T1468T,APC:NM_001354900:exon16:c.4356G>A:p.T1452T,APC:NM_001354903:exon16:c.4176G>A:p.T1392T,APC:NM_001354904:exon16:c.4101G>A:p.T1367T,APC:NM_001127510:exon17:c.4479G>A:p.T1493T,APC:NM_001354896:exon17:c.4533G>A:p.T1511T,APC:NM_001354906:exon17:c.3630G>A:p.T1210T rs41115 ID=COSV57321403;OCCURENCE=1(breast),2(liver),14(meninges),41(large_intestine),3(central_nervous_system),17(soft_tissue),2(lung) 51412 Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|not_specified|APC-Associated_Polyposis_Disorders|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.665535 0.8165 0.5862 0.6516 0.5315 0.7504 0.8238 0.5590 0.6171 0.6297 0.7184 0.5933 0.5356 0.6918 0.5927 0.8082 0.5563 0.6050 0.6209 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 358 2466 chr5 112175770 . G A 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2447;VD=1214;AF=0.4961;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47089;SOR=0.99422;LSEQ=ACTTTATTACATTTTGCCAC;RSEQ=GAAAGTACTCCAGATGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2447:1214:701,513:655,572:1227,1214:0.4961:2,2:38.3:1:34.9:1:0.03092:1.19:60:2428:0.5:0.0159:1.1 0/1:2466:1227:709,518:704,531:1235,1227:0.4976:2,2:38.1:1:34.9:1:0.71381:1.03:60:1226:0.5014:0.0187:1.1
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chr5 112176325 112176325 G A exonic APC . synonymous SNV APC:NM_001127511:exon14:c.4980G>A:p.G1660G,APC:NM_001354897:exon15:c.5064G>A:p.G1688G,APC:NM_001354899:exon15:c.4950G>A:p.G1650G,APC:NM_001354901:exon15:c.4857G>A:p.G1619G,APC:NM_001354902:exon15:c.4761G>A:p.G1587G,APC:NM_001354905:exon15:c.4554G>A:p.G1518G,APC:NM_000038:exon16:c.5034G>A:p.G1678G,APC:NM_001354895:exon16:c.5034G>A:p.G1678G,APC:NM_001354898:exon16:c.4959G>A:p.G1653G,APC:NM_001354900:exon16:c.4911G>A:p.G1637G,APC:NM_001354903:exon16:c.4731G>A:p.G1577G,APC:NM_001354904:exon16:c.4656G>A:p.G1552G,APC:NM_001127510:exon17:c.5034G>A:p.G1678G,APC:NM_001354896:exon17:c.5088G>A:p.G1696G,APC:NM_001354906:exon17:c.4185G>A:p.G1395G rs42427 ID=COSV57321627;OCCURENCE=14(meninges),33(large_intestine),3(central_nervous_system),2(lung) 51413 Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|not_specified|APC-Associated_Polyposis_Disorders|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.666733 0.8165 0.5901 0.6540 0.5359 0.7520 0.8246 0.5604 0.6212 0.6333 0.7183 0.5956 0.5373 0.6950 0.5927 0.8068 0.5573 0.6082 0.6255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 360 2642 chr5 112176325 . G A 360 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2436;VD=1210;AF=0.4967;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.34665;SOR=0.97654;LSEQ=GGAGAAGGAGTTAGAGGAGG;RSEQ=GCACAGTCAGGTGAATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2436:1210:742,468:768,451:1219,1210:0.4967:2,2:38.2:1:34.6:1:0.40288:1.07402:60:150.25:0.4994:0.0218:1.1 1/0:2642:1328:830,498:810,491:1301,1328:0.5026:2,2:37.7:1:34.7:1:0.90392:1.01:60:264.6:0.5069:0.0182:1.1
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chr5 112176559 112176559 T G exonic APC . synonymous SNV APC:NM_001127511:exon14:c.5214T>G:p.S1738S,APC:NM_001354897:exon15:c.5298T>G:p.S1766S,APC:NM_001354899:exon15:c.5184T>G:p.S1728S,APC:NM_001354901:exon15:c.5091T>G:p.S1697S,APC:NM_001354902:exon15:c.4995T>G:p.S1665S,APC:NM_001354905:exon15:c.4788T>G:p.S1596S,APC:NM_000038:exon16:c.5268T>G:p.S1756S,APC:NM_001354895:exon16:c.5268T>G:p.S1756S,APC:NM_001354898:exon16:c.5193T>G:p.S1731S,APC:NM_001354900:exon16:c.5145T>G:p.S1715S,APC:NM_001354903:exon16:c.4965T>G:p.S1655S,APC:NM_001354904:exon16:c.4890T>G:p.S1630S,APC:NM_001127510:exon17:c.5268T>G:p.S1756S,APC:NM_001354896:exon17:c.5322T>G:p.S1774S,APC:NM_001354906:exon17:c.4419T>G:p.S1473S rs866006 ID=COSV57321636;OCCURENCE=14(meninges),37(large_intestine),3(central_nervous_system),1(lung) 51415 Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|not_specified|APC-Associated_Polyposis_Disorders|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.666933 0.8165 0.5880 0.6537 0.5335 0.7508 0.8235 0.5603 0.6207 0.6297 0.7192 0.5942 0.5361 0.6933 0.5993 0.8055 0.5574 0.6065 0.6214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 344 2366 chr5 112176559 . T G 344 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2295;VD=1157;AF=0.5041;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09327;SOR=1.08233;LSEQ=GTCCAGCAAGCATCTGCGTC;RSEQ=TCTTCTGCACCCAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2295:1157:609,548:618,517:1135,1157:0.5041:2,2:37.9:1:33.9:1:0.40226:1.07559:60:47.208:0.5002:0.0218:1.1 0/1:2366:1146:620,526:632,583:1215,1146:0.4844:2,2:37.6:1:34.2:1:0.3222:1.09:60:62.667:0.4812:0.019:1.1
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chr5 112176756 112176756 T A exonic APC . nonsynonymous SNV APC:NM_001127511:exon14:c.5411T>A:p.V1804D,APC:NM_001354897:exon15:c.5495T>A:p.V1832D,APC:NM_001354899:exon15:c.5381T>A:p.V1794D,APC:NM_001354901:exon15:c.5288T>A:p.V1763D,APC:NM_001354902:exon15:c.5192T>A:p.V1731D,APC:NM_001354905:exon15:c.4985T>A:p.V1662D,APC:NM_000038:exon16:c.5465T>A:p.V1822D,APC:NM_001354895:exon16:c.5465T>A:p.V1822D,APC:NM_001354898:exon16:c.5390T>A:p.V1797D,APC:NM_001354900:exon16:c.5342T>A:p.V1781D,APC:NM_001354903:exon16:c.5162T>A:p.V1721D,APC:NM_001354904:exon16:c.5087T>A:p.V1696D,APC:NM_001127510:exon17:c.5465T>A:p.V1822D,APC:NM_001354896:exon17:c.5519T>A:p.V1840D,APC:NM_001354906:exon17:c.4616T>A:p.V1539D rs459552 ID=COSV57321643;OCCURENCE=1(lung),17(meninges),41(large_intestine),3(central_nervous_system) 33882 Hereditary_cancer-predisposing_syndrome|Familial_multiple_polyposis_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|not_specified|APC-Associated_Polyposis_Disorders|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021055,MedGen:C0032580,OMIM:PS175100,Orphanet:ORPHA733,SNOMED_CT:72900001|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.865415 0.9008 0.8263 0.7991 0.9584 0.8306 0.9024 0.6886 0.7690 0.7450 0.7867 0.8113 0.9616 0.8062 0.7767 0.8937 0.6910 0.7465 0.7719 0.672 0.045 T 0.000 0.469 N 0.981 0.250 P -0.895 0.014 N -2.3 0.877 D 0.59 0.026 N -0.947 0.415 T 0.000 0.000 T . . . . . 0.050 0.107 N c -0.653 -0.403 0.017 0.130 0.732 0.924 0 3.59 0.401 2.360 0.436 -0.197 0.102 0.997 0.399 0.991 0.552 9.399 0.374 . ENSG00000129625.8|ENSG00000212643.1|ENSG00000129625.8|ENSG00000153037.8 Esophagus_Muscularis|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Testis 5q22.2 0.5 351 2255 chr5 112176756 . T A 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2167;VD=1041;AF=0.4804;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12082;SOR=0.93028;LSEQ=TTTGAAAAATAATTCCAAGG;RSEQ=CTTCAATGATAAGCTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2167:1041:682,359:692,432:1124,1041:0.4804:2,2:39.3:1:34.7:1:0.06066:1.19:60:346:0.4817:0.0069:1.1 0/1:2255:1124:719,405:705,421:1126,1124:0.4984:2,2:38.4:1:34.7:1:0.51202:1.06:60:280:0.4993:0.0106:1.1
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chr5 112177171 112177171 G A exonic APC . synonymous SNV APC:NM_001127511:exon14:c.5826G>A:p.P1942P,APC:NM_001354897:exon15:c.5910G>A:p.P1970P,APC:NM_001354899:exon15:c.5796G>A:p.P1932P,APC:NM_001354901:exon15:c.5703G>A:p.P1901P,APC:NM_001354902:exon15:c.5607G>A:p.P1869P,APC:NM_001354905:exon15:c.5400G>A:p.P1800P,APC:NM_000038:exon16:c.5880G>A:p.P1960P,APC:NM_001354895:exon16:c.5880G>A:p.P1960P,APC:NM_001354898:exon16:c.5805G>A:p.P1935P,APC:NM_001354900:exon16:c.5757G>A:p.P1919P,APC:NM_001354903:exon16:c.5577G>A:p.P1859P,APC:NM_001354904:exon16:c.5502G>A:p.P1834P,APC:NM_001127510:exon17:c.5880G>A:p.P1960P,APC:NM_001354896:exon17:c.5934G>A:p.P1978P,APC:NM_001354906:exon17:c.5031G>A:p.P1677P rs465899 ID=COSV57321652;OCCURENCE=1(breast),14(meninges),44(large_intestine),3(central_nervous_system),2(lung) 51417 Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Familial_adenomatous_polyposis_1|Familial_colorectal_cancer|not_specified|APC-Associated_Polyposis_Disorders|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021056,MedGen:C2713442,OMIM:175100|MONDO:MONDO:0023113,MedGen:CN280943|MedGen:CN169374|MedGen:CN239210|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.666534 0.8165 0.5869 0.6517 0.5362 0.7501 0.8233 0.5593 0.6174 0.6315 0.7177 0.5952 0.5409 0.6938 0.5927 0.8097 0.5564 0.6055 0.6224 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q22.2 0.5 365 2877 chr5 112177171 . G A 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2778;VD=1365;AF=0.4914;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48304;SOR=1.00368;LSEQ=TTTGCTATTGAAAATACTCC;RSEQ=GTTTGCTTTTCTCATAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2778:1365:763,602:784,629:1413,1365:0.4914:2,2:36.4:1:34.9:1:0.84854:1.02:60:1364:0.4942:0.0148:1.1 0/1:2877:1411:724,687:800,660:1460,1411:0.4904:2,2:39.6:1:34.9:1:0.06682:1.15012:60:1410:0.493:0.0049:1.1
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chr5 131892979 131892979 G A intron RAD50 NM_005732:c.-38G>A . . rs4526098 ID=COSV99528532;OCCURENCE=18(meninges) . . . . . 0.92492 0.999 0.9187 0.9753 0.7611 0.9865 1 0.9997 0.9970 0.9856 0.9921 0.9302 0.7613 0.9845 1 1 1 0.9964 0.9888 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.1 1 379 1969 chr5 131892979 . G A 379 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2016;VD=2009;AF=0.9965;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40311;SOR=0.73071;LSEQ=CCTCAGTTAAGCCTTTGTGG;RSEQ=CTCCAGGTCCCTGGTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2016:2009:1343,666:0,0:0,2009:0.9965:0,2:39.9:1:34.6:1:1:0:60:199.9:0.999:0.0308:1.1 1/1:1969:1964:1377,587:0,0:0,1964:0.9975:0,2:40.6:1:34.3:1:1:0:60:80.833:0.999:0.0071:1.1
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chr5 131915213 131915213 G A intron RAD50 NM_005732:exon4:c.551+19G>A . . rs17166050 ID=COSV99528535;OCCURENCE=6(meninges) 251668 Nijmegen_breakage_syndrome-like_disorder|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013118,MedGen:C2751318,OMIM:613078,Orphanet:ORPHA240760|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.167732 0.1865 0.1759 0.1972 0.1166 0.1439 0.1682 0.2492 0.2107 0.2168 0.2239 0.1988 0.1184 0.1408 0.2583 0.1656 0.2596 0.2351 0.2280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.1 0.5 322 1176 chr5 131915213 . G A 322 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1204;VD=586;AF=0.4867;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14376;SOR=0.91343;LSEQ=AGGTTTGTAACCCTTAAATA;RSEQ=ACTTTGTAGTCCATTAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1204:586:227,359:269,348:617,586:0.4867:2,2:41:1:34.9:1:0.08958:1.22227:60:585:0.4924:0.0208:1.2 1/0:1176:599:239,360:238,339:577,599:0.5094:2,2:41.4:1:34.9:1:0.67758:1.05743:60:1198:0.5124:0.0306:1.2
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chr5 131924364 131924364 T - intron RAD50 NM_005732:exon8:c.1052-15T>- . . rs201800554 ID=COSV54755540;OCCURENCE=3(large_intestine) 983957 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.00579073 0.002 0.0314 0.0161 0.0208 0.0163 0.0200 0.0097 0.0168 0.0104 0.0128 0.0013 0.0042 0 0 0.0019 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.1 0.5 209 1747 chr5 131924363 . AT A 209 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1836;VD=63;AF=0.0343;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18977;SOR=1.20593;LSEQ=GTTGAAAAAAAAATTATGAG;RSEQ=TTTTTTTTTAAAAGGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1836:63:39,24:1217,553:1770,63:0.0343:2,2:39.9:1:35:1:0.26987:1.35409:60:126:0.0344:0.0033:0.2 0/1:1747:50:32,18:1174,521:1695,50:0.0286:2,2:40.6:1:35:1:0.43924:1.26729:60:100:0.0286:0.0029:0.1
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chr5 131925483 131925483 G C exonic RAD50 . nonsynonymous SNV RAD50:NM_005732:exon9:c.1406G>C:p.G469A rs55653181 . 212469 Hereditary_cancer-predisposing_syndrome MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009 criteria_provided,_multiple_submitters,_no_conflicts Uncertain_significance 0.000199681 . . 9.458e-06 0 0 0 0 1.844e-05 0 0 . . . . . . . . 0.517 0.073 T 0.000 0.843 D 1 0.810 D 2.28 0.651 M 3.33 0.062 T -0.57 0.172 N -1.025 0.221 T 0.024 0.101 T 0.010 0.264 T 0.09 0.010 0.984 0.827 D c 0.283 0.388 1.000 0.747 0.732 0.924 0 5.29 0.743 6.416 0.730 1.048 0.713 1.000 0.715 0.999 0.750 18.284 0.900 . . . 5q31.1 0.5 323 1284 chr5 131925483 . G C 323 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1413;VD=694;AF=0.4912;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24099;SOR=0.94445;LSEQ=TGAATTACAGCAGTTGGAAG;RSEQ=ATCTTCAGACAGGATTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1413:694:425,269:429,289:718,694:0.4912:2,2:38.7:1:34.3:1:0.5863:1.06:60:98.143:0.4942:0:1.1 1/0:1284:649:383,266:379,255:634,649:0.5055:2,2:39.6:1:34.6:1:0.82012:1.03223:60:323.5:0.5099:0.0093:1.1
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chr5 131927551 131927551 T - intron RAD50 NM_005732:exon11:c.1636-18T>- . . rs762814289 ID=COSV54750542;OCCURENCE=1(meninges),1(large_intestine),2(stomach) 487128 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . 0.0320 0.0227 0.0188 0.0250 0.0235 0.0076 0.0228 0.0143 0.0297 0.0001 0 0 0 0 0.0013 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.1 0.5 205 926 chr5 131927550 . AT A 205 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=940;VD=59;AF=0.0628;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.53346;SOR=1.00223;LSEQ=ATAGACTTTATTTTTAAAAG;RSEQ=TTTTTTTTTACCTATAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:940:59:48,11:652,229:881,59:0.0628:2,2:38.3:1:35:1:0.27958:1.53:60:118:0.0628:0.0064:0.1 0/1:926:58:43,15:645,219:864,58:0.0626:2,2:42:1:35:1:1:1.02737:60:116:0.0627:0.0022:0
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chr5 131931452 131931452 A - exonic RAD50 . frameshift deletion RAD50:NM_005732:exon13:c.2157delA:p.K722Rfs*14 rs1060501968 ID=COSV54748452;OCCURENCE=1(salivary_gland),1(breast),16(large_intestine),5(stomach),1(prostate) 394669 Nijmegen_breakage_syndrome-like_disorder|Hereditary_cancer-predisposing_syndrome MONDO:MONDO:0013118,MedGen:C2751318,OMIM:613078,Orphanet:ORPHA240760|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009 criteria_provided,_multiple_submitters,_no_conflicts Pathogenic . . . 0.0007 0.0010 0.0006 0.0009 0 0.0009 0.0015 0.0004 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.1 0.5 235 1943 chr5 131931451 . TA T 235 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2022;VD=96;AF=0.0475;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09779;SOR=0.8227;LSEQ=CAAGTCAACAGAATCAGAGC;RSEQ=AAAAAAAAGGAAAAGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2022:96:48,48:1114,808:1922,96:0.0475:2,2:39.4:1:35:1:0.1385:1.37847:60:192:0.0475:0.003:0.2 0/1:1943:111:64,47:1151,678:1829,111:0.0571:2,2:38.5:1:34.7:1:0.26794:1.24654:60:110:0.0571:0.0072:0.2
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chr5 131944382 131944382 A - exonic RAD50 . frameshift deletion RAD50:NM_005732:exon17:c.2794delA:p.N934Ifs*6 rs758740142 ID=COSV54751030;OCCURENCE=1(NS),1(haematopoietic_and_lymphoid_tissue),1(stomach),1(urinary_tract),2(prostate) 474257 Hereditary_cancer-predisposing_syndrome MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009 criteria_provided,_single_submitter Pathogenic . . . 0.0007 0.0009 0.0013 0.0012 0.0008 0.0007 0 0.0002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.1 0.5 148 916 chr5 131944381 . CA C 148 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=998;VD=19;AF=0.019;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53723;SOR=1.02631;LSEQ=GAAAAAGAAGAATTAATCAA;RSEQ=AAAAAAATACAAGCAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:998:19:11,8:561,417:978,19:0.019:2,2:44.9:1:35:1:1:1.02:60:38:0.019:0.001:0.1 0/1:916:17:9,8:508,391:899,17:0.0186:2,2:44.1:1:35:0:0.80848:1.15469:60:34:0.0186:0:0.1
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chr5 138132247 138132247 A GT intronic CTNNA1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.2 0.5 198 689 chr5 138132247 . A GT 198 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Complex;DP=700;VD=51;AF=0.0729;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.34901;SOR=0.90591;LSEQ=CGTCTCAAAAAAAAAAAAAA;RSEQ=AGTAGTAGGTATCTGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:51:38,13:422,202:624,51:0.0729:2,2:42:1:34.1:1:0.35119:1.40:60:102:0.0772:0:1.1 0/1:689:55:41,14:440,168:608,55:0.0798:2,2:41.9:1:34.4:1:0.87473:1.12:60:54:0.084:0:1.1
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chr5 138132255 138132255 G T intronic CTNNA1 . . . rs825753 . . . . . . 0.813498 0.9911 . . . . . . . . . 0.7029 0.7590 0.6710 0.6607 0.9910 0.6191 0.6559 0.6514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.2 0.5 278 725 chr5 138132255 . G T 278 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=724;VD=247;AF=0.3412;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27864;SOR=0.93173;LSEQ=AAAAAAAAAAAAAAGTAGTA;RSEQ=GTATCTGAGAAGAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:724:247:184,63:257,148:405,247:0.3412:2,2:42.8:1:34.7:1:0.00341:1.68:60:246:0.3856:0:1.4 0/1:725:259:183,76:284,116:400,259:0.3572:2,2:41.6:1:34.7:1:0.93027:1.01675:60:258:0.3988:0:1.3
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chr5 138204894 138204894 A T UTR3 LRRTM2 NM_015564:c.*3805T>A . . rs288040 ID=COSV51220408;OCCURENCE=1(liver) . . . . . 0.185503 0.0079 . . . . . . . . . 0.2618 0.2068 0.2488 0.3067 0.0006 0.2851 0.3159 0.2836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.2 0.5 287 773 chr5 138204894 . A T 287 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=721;VD=340;AF=0.4716;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.31731;SOR=1.05618;LSEQ=AAAAAACCGCTAAGGACAAA;RSEQ=ATGTTAGTTGAAAGAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:721:340:183,157:196,185:381,340:0.4716:2,2:41.8:1:32.8:1:0.55035:1.10:60:29.909:0.4653:0.0208:1.1 0/1:773:354:206,148:235,184:419,354:0.458:2,2:42.3:1:33.9:1:0.56058:1.09:60:58:0.4543:0.0155:1.1
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chr5 138258620 138258620 A - intronic CTNNA1 . . . rs34458033 . . . . . . 0.259784 0.0675 . . . . . . . . . 0.3287 0.3563 0.3077 0.3425 0.0073 0.4031 0.3405 0.3409 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q31.2 0.5 310 1235 chr5 138258619 . TA T 310 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1322;VD=481;AF=0.3638;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.42106;SOR=0.98047;LSEQ=TCAAGAAAGTCTAAATGGAT;RSEQ=AAAAAAAAAAAAACCGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1322:481:254,227:397,312:709,481:0.3638:2,2:43.7:1:34.9:1:0.28594:1.13705:60:962:0.3647:0.0204:0.1 0/1:1235:455:234,221:373,298:671,455:0.3684:2,2:44.1:1:34.9:1:0.18032:1.18196:60:910:0.3687:0.0243:0.2
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chr5 149435608 149435608 G C exonic CSF1R . synonymous SNV CSF1R:NM_001288705:exon18:c.2535C>G:p.L845L,CSF1R:NM_005211:exon19:c.2535C>G:p.L845L,CSF1R:NM_001349736:exon20:c.2535C>G:p.L845L rs56327604 ID=COSV53841688;OCCURENCE=4(meninges),1(soft_tissue) 302319 Hereditary_diffuse_leukoencephalopathy_with_spheroids|not_provided MONDO:MONDO:0009096,MedGen:C3711381,OMIM:221820,Orphanet:ORPHA313808,SNOMED_CT:702427005|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.0125799 . 0.0308 0.0325 0.0085 0.0216 0 0.0448 0.0496 0.0246 0.0077 0.0307 0.0105 0.0286 0.0132 0 0.0404 0.0432 0.0428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 356 2550 chr5 149435608 . G C 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2504;VD=1185;AF=0.4732;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2676;SOR=0.96413;LSEQ=CCAAGTGAGAAGATCTCCCA;RSEQ=AGGAGGATGCCATAGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2504:1185:777,408:900,413:1313,1185:0.4732:2,2:39.2:1:34.6:1:0.1148:1.14421:60:130.667:0.4734:0.0268:1.1 0/1:2550:1230:830,400:887,429:1316,1230:0.4824:2,2:40.5:1:34.7:1:1:1.00:60:245:0.484:0.0196:1.1
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chr5 149435759 149435759 G A intron CSF1R NM_001349736:exon19:c.2442+23C>T;NM_001288705:exon17:c.2442+23C>T;NM_005211:exon18:c.2442+23C>T . . rs216136 ID=COSV53827642;OCCURENCE=2(liver),16(meninges),1(stomach),3(haematopoietic_and_lymphoid_tissue),20(soft_tissue),1(lung) 1245342 Hereditary_diffuse_leukoencephalopathy_with_spheroids|Brain_abnormalities,_neurodegeneration,_and_dysosteosclerosis|not_provided MONDO:MONDO:0009096,MedGen:C3711381,OMIM:221820,Orphanet:ORPHA313808,SNOMED_CT:702427005|MONDO:MONDO:0032772,MedGen:C5193117,OMIM:618476|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.394169 0.4593 0.4593 0.5285 0.1706 0.4024 0.4473 0.6654 0.6129 0.5519 0.5156 0.4851 0.1749 0.4026 0.5167 0.4436 0.6663 0.6246 0.6029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 355 3353 chr5 149435759 . G A 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3418;VD=1616;AF=0.4728;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06791;SOR=0.92892;LSEQ=TTCACCCCCTCCCCAGCCTG;RSEQ=CCCAAGCCCTCCCAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3418:1616:944,672:1003,790:1793,1616:0.4728:2,2:37.9:1:33.4:1:0.14574:1.11:60:31.98:0.471:0.0079:1.1 0/1:3353:1647:926,721:962,739:1701,1647:0.4912:2,2:37.2:1:33.3:1:0.86167:1.01357:60:29.5:0.4878:0.0143:1.1
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chr5 149447806 149447808 AGC - exonic CSF1R . nonframeshift deletion CSF1R:NM_001288705:exon10:c.1596_1598del:p.L537del,CSF1R:NM_005211:exon11:c.1596_1598del:p.L537del,CSF1R:NM_001349736:exon12:c.1596_1598del:p.L537del rs755436912 ID=COSV99036304;OCCURENCE=1(stomach) . . . . . . . . 0.0003 0.0003 0.0002 0 0 0.0001 0.0015 0.0012 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 160 2209 chr5 149447805 . GAGC G 160 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2217;VD=25;AF=0.0113;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.4474;SOR=1.08394;LSEQ=TACTTGTACAATAGCAGCAG;RSEQ=AGCAGCAGCAGCAAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2217:25:14,11:1345,847:2192,25:0.0113:2,2:33.2:1:34.6:1:0.68042:1.24754:60:50:0.0114:0.0014:0.2 0/1:2209:23:14,9:1354,830:2184,23:0.0104:2,2:44.9:1:34.5:1:1:1.04867:60:46:0.0105:0:0.1
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chr5 149457678 149457678 G A exonic CSF1R . synonymous SNV CSF1R:NM_001288705:exon4:c.726C>T:p.T242T,CSF1R:NM_005211:exon5:c.726C>T:p.T242T,CSF1R:NM_001349736:exon6:c.726C>T:p.T242T rs2228422 ID=COSV53827656;OCCURENCE=1(breast),1(liver),14(meninges),2(haematopoietic_and_lymphoid_tissue),1(stomach),19(soft_tissue),4(lung),1(thyroid) 302347 Hereditary_diffuse_leukoencephalopathy_with_spheroids|Brain_abnormalities,_neurodegeneration,_and_dysosteosclerosis|not_provided MONDO:MONDO:0009096,MedGen:C3711381,OMIM:221820,Orphanet:ORPHA313808,SNOMED_CT:702427005|MONDO:MONDO:0032772,MedGen:C5193117,OMIM:618476|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.38738 0.2113 0.4807 0.5153 0.3155 0.4101 0.2131 0.6969 0.5800 0.4986 0.5550 0.4998 0.3213 0.4081 0.4404 0.1995 0.7034 0.5878 0.6099 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 365 2875 chr5 149457678 . G A 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2824;VD=1428;AF=0.5057;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48136;SOR=1.00389;LSEQ=GATCTGCAGGGACTGACCTT;RSEQ=GTGTTGTTGTGTTGGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2824:1428:830,598:835,557:1392,1428:0.5057:2,2:39.4:1:34.9:1:0.31959:1.08005:60:1427:0.5075:0.0035:1.1 1/0:2875:1451:893,558:883,540:1423,1451:0.5047:2,2:38.7:1:34.8:1:0.78821:1.02176:60:289.2:0.5059:0.0136:1.1
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chr5 149460553 149460553 A G exonic CSF1R . synonymous SNV CSF1R:NM_001288705:exon2:c.84T>C:p.P28P,CSF1R:NM_005211:exon3:c.84T>C:p.P28P,CSF1R:NM_001349736:exon4:c.84T>C:p.P28P rs216123 ID=COSV53831811;OCCURENCE=1(breast),1(liver),13(meninges),1(haematopoietic_and_lymphoid_tissue),1(stomach),2(lung) 302657 Hereditary_diffuse_leukoencephalopathy_with_spheroids|Brain_abnormalities,_neurodegeneration,_and_dysosteosclerosis|not_provided MONDO:MONDO:0009096,MedGen:C3711381,OMIM:221820,Orphanet:ORPHA313808,SNOMED_CT:702427005|MONDO:MONDO:0032772,MedGen:C5193117,OMIM:618476|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.335264 0.0893 0.4737 0.4848 0.2940 0.3473 0.0918 0.7050 0.5793 0.5304 0.4696 0.4814 0.2924 0.3696 0.4161 0.0927 0.7106 0.5803 0.5941 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 368 3386 chr5 149460553 . A G 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3406;VD=1597;AF=0.4689;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29268;SOR=0.97267;LSEQ=CCTGGCTTCACGACCAGCTC;RSEQ=GGGACACTGGGCTCTATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3406:1597:841,756:942,853:1795,1597:0.4689:2,2:37.6:1:34.7:1:0.91774:1.01:60:198.625:0.4691:0.0206:1.1 0/1:3386:1611:832,779:953,815:1768,1611:0.4758:2,2:38.5:1:34.6:1:0.1901:1.09481:60:178:0.4748:0:1.1
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chr5 149513626 149513626 T G intronic PDGFRB . . . rs11740355 . 1223848 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0529153 0.0139 . . . . . . . . . 0.0852 0.0179 0.0383 0.0695 0.0228 0.1572 0.1150 0.1194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 339 1865 chr5 149513626 . T G 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1867;VD=930;AF=0.4981;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38402;SOR=1.02169;LSEQ=TCACCACCAGCCACTAGCAC;RSEQ=TCAGCTTGGGGATAGGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1867:930:407,523:398,537:935,930:0.4981:2,2:41.7:1:34.4:1:0.60736:1.05:60:115.25:0.4981:0.0112:1.1 0/1:1865:919:370,549:413,528:941,919:0.4928:2,2:40.5:1:34.4:1:0.12116:1.16051:60:130.286:0.4938:0.0145:1.1
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chr5 149784088 149784089 GA - intronic CD74 . . . rs757735734 . . . . . . . . . . . . . . . . . 3.242e-05 0.0001 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5q32 0.5 182 2408 chr5 149784087 . GGA G 182 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2472;VD=37;AF=0.015;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.44941;SOR=1.06098;LSEQ=AAACCAAGAAGGAACAGACA;RSEQ=GAGAGAGAGAAGTGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2472:37:21,16:1523,910:2433,37:0.015:2,2:41.6:1:35:1:0.49581:1.27499:60:74:0.0153:0.0004:0.2 0/1:2408:34:24,10:1488,884:2372,34:0.0141:2,2:31.7:1:34.7:1:0.37786:1.43:60:68:0.0143:0.0042:0.1
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chr6 32782387 32782387 G A intron HLA-DOB NM_002120:exon3:c.362-9C>T . . rs2071475 . . . . . . 0.228435 0.2421 0.1930 0.2490 0.1516 0.4241 0.2569 0.2933 0.2173 0.2463 0.2561 0.2189 0.1464 0.3529 0.2781 0.2305 0.2801 0.2336 0.2710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 357 2507 chr6 32782387 . G A 357 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2416;VD=1168;AF=0.4834;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32725;SOR=0.97321;LSEQ=CCTCTGGTTGCACTAGGAAG;RSEQ=GAGGAAAAATGAGACACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2416:1168:495,673:598,647:1245,1168:0.4834:2,2:39.5:1:34.9:1:0.00542:1.2565:60:583:0.4864:0.0199:1.1 0/1:2507:1229:555,674:609,669:1278,1229:0.4902:2,2:40.6:1:34.8:1:0.21456:1.10545:60:408.667:0.4926:0.0179:1.1
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chr6 32790099 32790099 - A intron TAP2 NM_018833:exon12:c.1933-4->T . . rs142246255 ID=COSV66498381;OCCURENCE=5(biliary_tract) 390598 not_specified MedGen:CN169374 criteria_provided,_single_submitter Benign . . 0.1113 0.1465 0.1265 0.0711 0.0958 0.075 0.1400 0.2059 0.1895 0.0498 0.0627 0.0265 0.0391 0.0415 0.0954 0.0384 0.0540 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 250 1502 chr6 32790099 . G GA 250 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1586;VD=145;AF=0.0914;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.34032;SOR=1.06198;LSEQ=AACTTCCAAAGGGTTTTCTA;RSEQ=AAAAAAAAAACAAAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1586:145:72,73:559,633:1192,145:0.0914:2,2:46.2:1:34.9:1:0.53867:1.12:60:290:0.1262:0:0.1 0/1:1502:130:50,79:557,654:1211,130:0.0866:2,2:48.8:1:34.7:1:0.13641:1.34536:60:129:0.108:0.0007:0.1
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chr6 32790110 32790111 CA AC splicing TAP2 NM_018833:exon12:r.spl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.25 129 1376 chr6 32790110 . CA AC 129 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Complex;DP=1464;VD=13;AF=0.0089;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.43514;SOR=0.87166;LSEQ=GGTTTTCTAGAAAAAAAAAA;RSEQ=AAAAAAACCCCTTGATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1464:13:8,5:621,751:1372,13:0.0089:2,2:7.5:1:33.5:1:0.27281:1.93:60:26:0.0098:0.0082:0.5 0/1:1376:14:7,7:568,714:1282,14:0.0102:2,2:15.7:1:34:1:0.78871:1.26:60:28:0.0109:0.0087:0.5
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chr6 32797684 32797684 A G intron TAP2 NM_018833:exon10:c.1795+23T>C;NM_001290043:exon10:c.1795+23T>C;NM_000544:exon10:c.1795+23T>C . . rs241437 ID=COSV66498022;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),2(upper_aerodigestive_tract) . . . . . 0.409345 0.5377 0.3498 0.4151 0.2716 0.4728 0.5520 0.4410 0.3840 0.4052 0.4706 0.3815 0.2761 0.4582 0.5033 0.5385 0.4407 0.4013 0.4408 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 347 2199 chr6 32797684 . A G 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2231;VD=1075;AF=0.4818;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37611;SOR=0.97942;LSEQ=TCTTTTTTACTGAAGGAGCA;RSEQ=GCTTACAATTTGTAGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2231:1075:712,363:758,392:1150,1075:0.4818:2,2:39.9:1:34.5:1:0.89311:1.01:60:88.583:0.4812:0.0148:1.5 0/1:2199:1071:688,383:705,414:1119,1071:0.487:2,2:40:1:34.6:1:0.56369:1.05:60:266.75:0.4903:0.0168:1.5
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chr6 32797809 32797809 C T exonic TAP2 . nonsynonymous SNV TAP2:NM_001290043:exon10:c.1693G>A:p.A565T,TAP2:NM_018833:exon10:c.1693G>A:p.A565T rs2228396 ID=COSV66498340;OCCURENCE=1(lung) 1155336 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0796725 0.0923 0.0981 0.0799 0.1195 0.0952 0.0985 0.0808 0.0861 0.0510 0.0213 0.1001 0.1192 0.0907 0.0497 0.1227 0.0736 0.0953 0.0855 0.229 0.233 T 0.046 0.235 N . . . 1.235 0.309 L -2.72 0.906 D -1.16 0.297 N -0.810 0.546 T 0.304 0.675 T . . . . . 0.071 0.130 N c -0.695 -0.693 1.000 0.489 0.707 0.730 0 1.47 0.217 -0.638 0.055 -0.477 0.053 0.000 0.063 0.643 0.297 6.970 0.237 AAA+ ATPase domain|ABC transporter-like|P-loop containing nucleoside triphosphate hydrolase . . 6p21.32 0.5 365 2920 chr6 32797809 . C T 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2900;VD=1439;AF=0.4962;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47841;SOR=0.9958;LSEQ=GCAGCTCTGCAGCCCATAAG;RSEQ=AATGTTGTTCCTCACAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2900:1439:735,704:765,695:1460,1439:0.4962:2,2:38.4:1:34.8:1:0.48029:1.05425:60:286.8:0.4971:0.0179:1.1 0/1:2920:1452:755,697:769,695:1464,1452:0.4973:2,2:39:1:34.8:1:0.79524:1.02147:60:483:0.4998:0.0185:1.1
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chr6 32797876 32797876 A - intron TAP2 NM_018833:exon10:c.1636-10T>-;NM_001290043:exon10:c.1636-10T>-;NM_000544:exon10:c.1636-10T>- . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 198 2551 chr6 32797875 . CA C 198 p8 STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2554;VD=27;AF=0.0106;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00407;SOR=0.52382;LSEQ=AACTGAAACCACCTGTGCAG;RSEQ=GGGACAGGGGCAGAGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2554:27:12,15:653,676:1329,27:0.0106:2,2:7.3:1:34.3:1:0.69967:1.2073:60:54:0.0107:0.0094:1 0/1:2551:51:22,29:682,637:1319,51:0.02:2,2:4.6:1:35:1:0.25477:1.41094:60:102:0.0202:0.0188:1.1
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chr6 32797876 32797876 A G intron TAP2 NM_018833:exon10:c.1636-10T>C;NM_001290043:exon10:c.1636-10T>C;NM_000544:exon10:c.1636-10T>C . . rs241436 ID=COSV66498026;OCCURENCE=1(large_intestine),2(central_nervous_system),2(haematopoietic_and_lymphoid_tissue),1(lung) 389758 Bare_lymphocyte_syndrome_type_1|not_specified|not_provided MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.434305 0.5496 0.4005 0.4824 0.2645 0.5482 0.5476 0.5671 0.4733 0.5233 0.5058 0.4375 0.2675 0.5239 0.6358 0.5409 0.5579 0.4824 0.5266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 352 2551 chr6 32797876 . A G 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2554;VD=1182;AF=0.4628;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42632;SOR=1.01208;LSEQ=ACTGAAACCACCTGTGCAGC;RSEQ=GGGACAGGGGCAGAGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2554:1182:576,606:653,676:1329,1182:0.4628:2,2:40.3:1:34.5:1:0.84164:1.01628:60:89.923:0.4622:0:1.1 0/1:2551:1173:585,588:682,637:1319,1173:0.4598:2,2:40:1:34.5:1:0.37723:1.0761:60:96.75:0.4594:0:1.1
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chr6 32800412 32800412 C T exonic TAP2 . nonsynonymous SNV TAP2:NM_001290043:exon6:c.1135G>A:p.V379I,TAP2:NM_018833:exon6:c.1135G>A:p.V379I rs1800454 ID=COSV66499344;OCCURENCE=1(breast),1(haematopoietic_and_lymphoid_tissue),1(prostate) 28763 PEPTIDE_TRANSPORTER_PSF2_POLYMORPHISM|Bare_lymphocyte_syndrome_type_1|not_specified|not_provided .|MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.145966 0.1905 0.1413 0.1437 0.1509 0.1747 0.1977 0.1411 0.1457 0.1268 0.0878 0.1520 0.1508 0.1711 0.1093 0.2085 0.1328 0.1512 0.1459 0.488 0.080 T 0.122 0.027 N . . . -0.345 0.033 N -2.39 0.884 D 0.23 0.046 N -0.903 0.477 T 0.073 0.295 T . . . . . 0.002 0.011 N c -2.385 -2.397 1.000 0.747 0.732 0.924 0 -9.93 0.004 -2.534 0.010 -2.671 0.002 0.000 0.063 0.000 0.016 1.346 0.020 ABC transporter type 1, transmembrane domain ENSG00000213676.6|ENSG00000213676.6 Cells_Transformed_fibroblasts|Heart_Left_Ventricle 6p21.32 0.5 361 2651 chr6 32800412 . C T 361 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2671;VD=1322;AF=0.4949;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13608;SOR=0.94017;LSEQ=CTGGTATCTTACCCTCCTTA;RSEQ=GAGCAGGTACAAGGCGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2671:1322:784,538:775,571:1346,1322:0.4949:2,2:39.5:1:34.9:1:0.36659:1.07:60:660:0.4981:0.0183:1.1 1/0:2651:1353:744,609:735,560:1295,1353:0.5104:2,2:38.1:1:34.8:1:0.36809:1.07432:60:269.6:0.5114:0.0207:1.1
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chr6 32805470 32805470 C G intron TAP2 NM_018833:exon2:c.493+48G>C;NM_018833:exon3:c.494-42G>C;NM_001290043:exon2:c.493+48G>C;NM_001290043:exon3:c.494-42G>C;NM_000544:exon2:c.493+48G>C;NM_000544:exon3:c.494-42G>C . . rs2071465 ID=COSV66487493;OCCURENCE=1(breast),3(haematopoietic_and_lymphoid_tissue),2(lung) 1325895 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.398163 0.3353 0.4158 0.4045 0.4027 0.3090 0.3014 0.3702 0.4268 0.3746 0.4614 0.3978 0.4103 0.3222 0.3859 0.2888 0.3805 0.4107 0.3996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 360 2774 chr6 32805470 . C G 360 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2851;VD=1432;AF=0.5023;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07463;SOR=1.0815;LSEQ=ACACAAGAATGTGCTGGTGC;RSEQ=CAGGCCCTTTTACCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2851:1432:822,610:803,608:1411,1432:0.5023:2,2:38.1:1:34.4:1:0.82011:1.02:60:109.154:0.5037:0.02:1.1 0/1:2774:1339:752,587:826,601:1427,1339:0.4827:2,2:37.8:1:34.5:1:0.37676:1.07279:60:147.778:0.4866:0.0209:1.1
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chr6 32814902 32814902 C T exonic TAP1 . synonymous SNV TAP1:NM_000593:exon10:c.2163G>A:p.P721P,TAP1:NM_001292022:exon10:c.1380G>A:p.P460P rs41551515 . 455510 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0269569 0.003 0.0291 0.0299 0.0283 0.0133 0.0006 0.0330 0.0346 0.0277 0.0395 0.0306 0.0328 0.0119 0.0166 0 0.0341 0.0329 0.0348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 362 2802 chr6 32814902 . C T 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2784;VD=1335;AF=0.4795;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44306;SOR=0.99094;LSEQ=TCATCCAGGATAAGTACACA;RSEQ=GGTTTCCGGATCAATGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2784:1335:729,606:807,638:1445,1335:0.4795:2,2:40.1:1:34.9:1:0.51657:1.05142:60:666.5:0.4814:0.0122:1.7 0/1:2802:1350:702,648:801,647:1448,1350:0.4818:2,2:40.2:1:34.9:1:0.08103:1.14273:60:674:0.4835:0.0103:1.7
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chr6 32814975 32814975 T C exonic TAP1 . nonsynonymous SNV TAP1:NM_000593:exon10:c.2090A>G:p.D697G,TAP1:NM_001292022:exon10:c.1307A>G:p.D436G rs1135216 ID=COSV62754137;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),3(soft_tissue),2(lung),1(thyroid) 28769 PEPTIDE_TRANSPORTER_PSF1_POLYMORPHISM|Bare_lymphocyte_syndrome_type_1|not_specified .|MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.191494 0.1319 0.1700 0.1767 0.2361 0.1922 0.1581 0.1738 0.1550 0.1720 0.2176 0.1787 0.2366 0.1599 0.1854 0.1669 0.1762 0.1488 0.1636 1.0 0.010 T 0.000 0.491 N 0.000 0.810 P -1.275 0.007 N -2.37 0.882 D 5.78 0.000 N -1.000 0.300 T 0.107 0.389 T . . . . . 0.066 0.125 N c -0.822 -0.520 1.000 0.747 0.737 0.974 0 5.43 0.789 5.482 0.663 0.063 0.168 1.000 0.715 0.206 0.219 12.235 0.536 AAA+ ATPase domain|ABC transporter-like|P-loop containing nucleoside triphosphate hydrolase ENSG00000168394.9|ENSG00000198502.5|ENSG00000198502.5|ENSG00000196126.6|ENSG00000198502.5|ENSG00000196126.6|ENSG00000198502.5 Artery_Tibial|Breast_Mammary_Tissue|Colon_Sigmoid|Colon_Sigmoid|Thyroid|Thyroid|Whole_Blood 6p21.32 0.5 358 2694 chr6 32814975 . T C 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2617;VD=1252;AF=0.4784;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20729;SOR=0.95472;LSEQ=ACAGCTGGCTCCCAGCCTCG;RSEQ=CTACCTCTGCAGAGCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2617:1252:647,605:702,657:1359,1252:0.4784:2,2:35.6:1:34.4:1:1:1.00:60:88.429:0.4774:0.0279:1.7 0/1:2694:1320:685,635:700,663:1363,1320:0.49:2,2:35.7:1:34.6:1:0.78691:1.02:60:119:0.4904:0.0264:1.7
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chr6 32816443 32816443 C T exonic TAP1 . nonsynonymous SNV TAP1:NM_000593:exon7:c.1732G>A:p.V578I,TAP1:NM_001292022:exon7:c.949G>A:p.V317I rs41561219 . 455623 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0265575 0.003 0.0279 0.0297 0.0264 0.0130 0.0006 0.0330 0.0344 0.0274 0.0402 0.0304 0.0321 0.0119 0.0167 0 0.0341 0.0330 0.0348 0.465 0.086 T 0.078 0.211 N 1 0.090 N 1.375 0.344 L -2.67 0.903 D -0.56 0.170 N -0.848 0.521 T 0.213 0.574 T . . . . . 0.148 0.184 N c -1.062 -1.022 1.000 0.446 0.732 0.924 0 3.25 0.362 0.462 0.215 0.011 0.139 0.001 0.137 0.002 0.062 4.473 0.111 ABC transporter-like|P-loop containing nucleoside triphosphate hydrolase ENSG00000204264.4|ENSG00000204261.4 Whole_Blood|Whole_Blood 6p21.32 0.5 358 2506 chr6 32816443 . C T 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2563;VD=1240;AF=0.4838;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05395;SOR=0.91219;LSEQ=TTGTACCTGTAGCACTAAGA;RSEQ=ATCTGGGCGGTTTGGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2563:1240:807,433:841,479:1320,1240:0.4838:2,2:39.3:1:34.9:1:0.48282:1.06:60:412.333:0.4847:0.0094:1.1 1/0:2506:1270:834,436:813,421:1234,1270:0.5068:2,2:39.9:1:34.8:1:0.93287:1.00955:60:422.333:0.5078:0.0132:1.1
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chr6 32818236 32818236 G A exonic TAP1 . nonsynonymous SNV TAP1:NM_000593:exon5:c.1289C>T:p.A430V,TAP1:NM_001292022:exon5:c.506C>T:p.A169V rs2127679 . 455637 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0265575 0.003 0.0279 0.0297 0.0264 0.0130 0.0006 0.0330 0.0343 0.0274 0.0402 0.0303 0.0320 0.0120 0.0166 0 0.0341 0.0328 0.0327 0.575 0.061 T 0.067 0.218 N 1 0.810 D -0.07 0.048 N -2.58 0.898 D -0.35 0.129 N -1.029 0.207 T 0.178 0.524 T . . . . . 0.826 0.415 D c -0.509 -0.311 1.000 0.454 0.722 0.854 0 1.7 0.232 3.943 0.561 0.128 0.215 1.000 0.715 0.831 0.347 9.256 0.366 ABC transporter type 1, transmembrane domain ENSG00000204264.4|ENSG00000204261.4 Whole_Blood|Whole_Blood 6p21.32 0.5 359 2695 chr6 32818236 . G A 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2717;VD=1304;AF=0.4799;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27797;SOR=0.96703;LSEQ=CTGTAGGCATGGCCGACAGA;RSEQ=CCTCAATGGCCACCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2717:1304:681,623:688,718:1406,1304:0.4799:2,2:38.2:1:34.7:1:0.09073:1.14:60:325:0.4818:0.0066:1.1 0/1:2695:1316:682,634:710,666:1376,1316:0.4883:2,2:38.8:1:34.7:1:0.90793:1.01:60:262.2:0.4897:0:1.1
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chr6 32818774 32818774 T C exonic TAP1 . nonsynonymous SNV TAP1:NM_000593:exon4:c.1177A>G:p.I393V,TAP1:NM_001292022:exon4:c.394A>G:p.I132V rs1057141 ID=COSV62754145;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),3(soft_tissue),1(lung) 28768 PEPTIDE_TRANSPORTER_PSF1_POLYMORPHISM|Bare_lymphocyte_syndrome_type_1|not_specified .|MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.228235 0.2083 0.1961 0.2077 0.2664 0.1878 0.2195 0.2023 0.1815 0.1948 0.2750 0.2059 0.2690 0.1671 0.2185 0.2379 0.2017 0.1692 0.1990 0.683 0.044 T 0.668 0.060 N 0.998 0.221 P -0.37 0.031 N -2.6 0.899 D -0.22 0.105 N -0.969 0.375 T 0.162 0.498 T . . . . . 0.027 0.073 N c -1.347 -1.326 1.000 0.747 0.707 0.730 0 -2.4 0.062 -1.180 0.032 -0.312 0.078 0.000 0.063 0.777 0.329 3.373 0.068 ABC transporter type 1, transmembrane domain ENSG00000168394.9|ENSG00000196126.6|ENSG00000204264.4 Artery_Tibial|Colon_Sigmoid|Whole_Blood 6p21.32 0.5 363 3204 chr6 32818774 . T C 363 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3281;VD=1597;AF=0.4867;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41549;SOR=0.98823;LSEQ=GAAAAGCAGAGGCAGGGTGA;RSEQ=CAGGGTGACCATGGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3281:1597:1010,587:1058,618:1676,1597:0.4867:2,2:38:1:34.2:1:0.97108:1.01:60:75.048:0.4861:0.0198:1.2 0/1:3204:1569:986,583:1014,615:1629,1569:0.4897:2,2:38.3:1:34.2:1:0.74231:1.03:60:86.167:0.4891:0.0187:1.2
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chr6 32819836 32819836 T A intron TAP1 NM_000593:exon3:c.1024+50A>T;NM_001292022:exon3:c.241+50A>T . . rs116106014 . . . . . . 0.0119808 0.002 0.0190 0.0221 0.0039 0.0125 0.0004 0.0327 0.0324 0.0190 0.0104 0.0218 0.0058 0.0108 0.0132 0 0.0341 0.0308 0.0319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 337 1616 chr6 32819836 . T A 337 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1729;VD=828;AF=0.4789;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39904;SOR=0.98009;LSEQ=GGGAGATCAAAGCAGATGTA;RSEQ=GAGGATATGAACAGTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1729:828:630,198:717,182:899,828:0.4789:2,2:36.8:1:34.8:1:0.0715:1.23799:60:413:0.4797:0.0202:2.4 0/1:1616:782:640,142:671,161:832,782:0.4839:2,2:37.2:1:34.6:1:0.56617:1.08:60:194.5:0.4838:0.0192:2.4
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chr6 32819854 32819854 A G intron TAP1 NM_000593:exon3:c.1024+32T>C;NM_001292022:exon3:c.241+32T>C . . rs72860338 . . . . . . 0.0265575 0.003 0.0284 0.0297 0.0267 0.0131 0.0006 0.0330 0.0346 0.0277 0.0397 0.0304 0.0321 0.0119 0.0166 0 0.0341 0.0328 0.0348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 341 1884 chr6 32819854 . A G 341 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1960;VD=927;AF=0.473;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19628;SOR=0.94434;LSEQ=TATGAGGATATGAACAGTAC;RSEQ=TGGCGTATAATGAAAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1960:927:669,258:780,252:1032,927:0.473:2,2:39.8:1:34.6:1:0.08898:1.19357:60:462.5:0.4727:0:2.3 0/1:1884:918:713,205:746,218:964,918:0.4873:2,2:37.6:1:34.5:1:0.91206:1.02:60:182.6:0.4869:0.0165:2.3
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chr6 32819968 32819968 G A exonic TAP1 . synonymous SNV TAP1:NM_000593:exon3:c.942C>T:p.G314G,TAP1:NM_001292022:exon3:c.159C>T:p.G53G rs41549617 . 455641 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0329473 0.005 0.0305 0.0343 0.0305 0.0142 0.0008 0.0330 0.0347 0.0306 0.0659 0.0314 0.0355 0.0131 0.0166 0 0.0338 0.0328 0.0357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 351 2640 chr6 32819968 . G A 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2721;VD=1327;AF=0.4877;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42832;SOR=1.01143;LSEQ=TGCAAGTGGCTGTGCACGTG;RSEQ=CCCATGGTGTTGTTATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2721:1327:714,613:760,629:1389,1327:0.4877:2,2:38.9:1:33.9:1:0.64396:1.03736:60:44.759:0.4861:0.0118:1.9 0/1:2640:1280:718,562:771,580:1351,1280:0.4848:2,2:39.7:1:34:1:0.63681:1.0405:60:54.652:0.4876:0.0148:1.9
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chr6 32820043 32820043 A G intron TAP1 NM_000593:exon3:c.894-27T>C;NM_001292022:exon3:c.111-27T>C . . rs72860339 . . . . . . 0.0329473 0.005 0.0302 0.0343 0.0305 0.0142 0.0008 0.0330 0.0346 0.0306 0.0658 0.0315 0.0355 0.0131 0.0166 0 0.0341 0.0330 0.0357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 355 2591 chr6 32820043 . A G 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2670;VD=1287;AF=0.482;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39948;SOR=0.98454;LSEQ=AGAACCCGGAAAAAAAGGGG;RSEQ=TCAGGGTGTGTTCAGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2670:1287:691,596:755,620:1375,1287:0.482:2,2:38.7:1:34.4:1:0.53356:1.05027:60:106.25:0.4819:0.009:1.9 0/1:2591:1259:699,560:681,642:1323,1259:0.4859:2,2:39.5:1:34.2:1:0.04023:1.18:60:58.952:0.4851:0.01:1.9
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chr6 32820799 32820799 C A intron TAP1 NM_000593:exon1:c.778+17G>T . . rs55967815 . 1155345 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0279553 0.004 0.0257 0.0418 0.0375 0.0182 0.0008 0.0537 0.0460 0.0303 0.0602 0.0297 0.0301 0.0120 0.0132 0 0.0338 0.0327 0.0336 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 338 2288 chr6 32820799 . C A 338 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2231;VD=1046;AF=0.4688;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27555;SOR=0.96337;LSEQ=CCTTGTGTCCTCCCCTCTTG;RSEQ=CCTGCGTTCCCCTTACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2231:1046:698,348:788,388:1176,1046:0.4688:2,2:38.9:1:33.2:1:0.89235:1.01255:60:28.056:0.465:0.0031:1.1 0/1:2288:1094:721,373:769,419:1188,1094:0.4781:2,2:38.3:1:33.5:1:0.56738:1.05:60:35.467:0.4763:0.0162:1.1
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chr6 32820991 32820991 A G exonic TAP1 . synonymous SNV TAP1:NM_000593:exon1:c.603T>C:p.V201V rs55702652 . 456369 Bare_lymphocyte_syndrome_type_1 MONDO:MONDO:0011476,MedGen:C1858266,OMIM:604571,Orphanet:ORPHA34592 criteria_provided,_single_submitter Benign 0.0333466 0.005 0.0300 0.0432 0.0386 0.0179 0.0010 0.0480 0.0447 0.0378 0.0729 0.0317 0.0359 0.0131 0.0166 0 0.0341 0.0334 0.0347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6p21.32 0.5 366 3303 chr6 32820991 . A G 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3359;VD=1645;AF=0.4897;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32299;SOR=1.02401;LSEQ=AGTGCCGCTGCATAACTGAC;RSEQ=ACGAAGGCGGTAGGGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3359:1645:979,666:924,780:1704,1645:0.4897:2,2:37.6:1:34.3:1:0.00214:1.24:60:116.5:0.4892:0.0217:1.2 0/1:3303:1598:914,684:1007,688:1695,1598:0.4838:2,2:37.8:1:34.3:1:0.20309:1.09531:60:98.875:0.4822:0.03:1.1
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chr6 41903782 41903782 A C exonic CCND3 . nonsynonymous SNV CCND3:NM_001136125:exon4:c.559T>G:p.S187A,CCND3:NM_001136126:exon4:c.187T>G:p.S63A,CCND3:NM_001136017:exon5:c.532T>G:p.S178A,CCND3:NM_001287427:exon5:c.625T>G:p.S209A,CCND3:NM_001287434:exon5:c.187T>G:p.S63A,CCND3:NM_001760:exon5:c.775T>G:p.S259A rs1051130 ID=COSV57827647;OCCURENCE=1(breast),1(biliary_tract),2(urinary_tract),20(soft_tissue),1(pancreas),1(thyroid) . . . . . 0.592452 0.504 0.6243 0.5419 0.8059 0.4456 0.5308 0.5457 0.5447 0.5058 0.4557 0.6191 0.8028 0.5263 0.5530 0.5374 0.5381 0.5524 0.5277 0.561 0.077 T 0.168 0.174 N 1 0.090 P 0.205 0.094 N 1.93 0.229 T -0.45 0.148 N -0.932 0.439 T 0.010 0.036 T . . . . . 0.172 0.196 N c -1.295 -1.257 1.000 0.747 0.722 0.854 0 0.192 0.143 0.143 0.158 0.038 0.153 0.002 0.151 0.074 0.178 8.226 0.306 Cyclin, C-terminal domain;Cyclin, C-terminal domain|Cyclin-like;Cyclin, N-terminal|Cyclin-like ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124593.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124593.10|ENSG00000124593.10|ENSG00000124641.10|ENSG00000124641.10|ENSG00000124641.10 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Artery_Aorta|Artery_Tibial|Artery_Tibial|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Colon_Transverse|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Heart_Left_Ventricle|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Stomach|Thyroid 6p21.1 0.5 365 3124 chr6 41903782 . A C 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3144;VD=1586;AF=0.5045;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18137;SOR=1.04836;LSEQ=TGGGCTGGAGCTGGTCTGAG;RSEQ=GGCTTCCCTGAGGCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3144:1586:832,754:789,754:1543,1586:0.5045:2,2:38.7:1:34.4:1:0.47425:1.05:60:143.182:0.5068:0.021:1.1 0/1:3124:1539:766,773:809,759:1568,1539:0.4926:2,2:37.7:1:34.5:1:0.31515:1.07559:60:117.385:0.4937:0.0234:1.1
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chr6 114281018 114281018 A - intronic HDAC2 . . . . ID=COSV64037615;OCCURENCE=1(large_intestine),1(biliary_tract) . . . . . . . . . . . . . . . . 3.354e-05 0 0.0013 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q21 0.5 213 1349 chr6 114281017 . TA T 213 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1277;VD=63;AF=0.0493;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.41734;SOR=0.94819;LSEQ=AGACAAAGTTTCACAGTAGC;RSEQ=AAAAAAAATAAAAAAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1277:63:44,19:823,388:1211,63:0.0493:2,2:38.7:1:34.9:1:0.88986:1.09:60:126:0.0493:0.0055:0.2 0/1:1349:70:51,19:886,391:1277,70:0.0519:2,2:37.3:1:34.9:1:0.59531:1.18:60:140:0.0519:0.0067:0.1
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chr6 114292040 114292040 T - exonic HDAC2 . frameshift deletion HDAC2:NM_001527:exon1:c.33delA:p.V12Sfs*20 rs759078191 ID=COSV64037484;OCCURENCE=21(large_intestine),2(haematopoietic_and_lymphoid_tissue),2(stomach),1(pancreas),1(prostate),1(upper_aerodigestive_tract),1(endometrium) . . . . . . . 0.0159 0.0018 0.0042 0 0 0 0.0029 0 0.0015 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q21 0.5 232 2556 chr6 114292039 . CT C 232 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2707;VD=96;AF=0.0355;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16095;SOR=0.85829;LSEQ=ACCGTCGTAGTAGTAGCAGA;RSEQ=TTTTTTTTGCCGCCTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2707:96:60,36:1643,959:2602,96:0.0355:2,2:40.9:1:34.8:1:0.91444:1.02795:60:192:0.0355:0.003:0.3 0/1:2556:105:71,34:1539,905:2444,105:0.0411:2,2:43.8:1:34.7:1:0.35412:1.23:60:210:0.0412:0.0027:0.3
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chr6 114292110 114292112 CTG - ncRNA_intronic HDAC2-AS2 . . . rs777539281 ID=COSV64037249;OCCURENCE=1(salivary_gland),1(breast),4(large_intestine),3(haematopoietic_and_lymphoid_tissue),1(soft_tissue) . . . . . . . 0.0950 0.0325 0.0665 0.0568 0.0369 0.0298 0.0462 0.0328 0.0232 0.0146 0.0196 0.0025 0 0.0006 0.0082 0.0162 0.0063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q21 0.5 244 3114 chr6 114292109 . CCTG C 244 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3245;VD=123;AF=0.0379;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.18119;SOR=0.88306;LSEQ=GCCGCCACCGGGCTCCTCCT;RSEQ=CTGCTGCTGCTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3245:123:59,64:1707,1398:3105,123:0.0379:2,2:44.5:1:35:1:0.13949:1.32438:60:246:0.0384:0.0015:0.3 0/1:3114:133:65,68:1612,1357:2969,133:0.0427:2,2:44.4:1:34.6:1:0.24761:1.24265:60:266:0.0433:0.001:0.3
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chr6 114292112 114292112 G C ncRNA_intronic HDAC2-AS2 . . . rs764249665 ID=COSV64037383;OCCURENCE=6(large_intestine),1(stomach),2(pancreas),1(prostate),1(thyroid) . . . . . . . . 9.839e-05 0 0 0 0 0.0003 0 0 3.31e-05 0.0001 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q21 0.5 183 3082 chr6 114292112 . G C 183 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=3220;VD=47;AF=0.0146;SHIFT3=0;MSI=8.000;MSILEN=3;SSF=0.12621;SOR=1.32783;LSEQ=GCCACCGGGCTCCTCCTCCT;RSEQ=CTGCTGCTGCTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3220:47:23,24:1670,1364:3034,47:0.0146:2,2:33:1:33:1:0.46085:1.27746:60:14.667:0.0146:0:1.2 0/1:3082:34:18,16:1577,1331:2908,34:0.011:2,2:34.2:1:34:1:1:1.05319:60:33:0.0114:0.0006:1.1
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chr6 117631463 117631463 - TAA intron ROS1 NM_002944:exon40:c.6234-19->TTA . . rs398048790 . . . . . . 0.0283546 0.0774 0.1475 0.1795 0.1288 0.3194 0.2130 0.1927 0.1434 0.1986 0.1995 0.2212 0.1891 0.3503 0.2219 0.3917 0.2708 0.2026 0.2433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 291 814 chr6 117631463 . T TTAA 291 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=815;VD=278;AF=0.3411;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.00491;SOR=0.7633;LSEQ=CCCTGTGGCAGAAGTTATAT;RSEQ=TAATAATAATAATAATAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:278:104,173:161,283:444,278:0.3411:2,2:49.1:1:34.7:1:0.75105:1.06:60:277:0.6253:0:0.1 0/1:814:329:141,188:159,248:407,329:0.4042:2,2:48.3:1:34.9:1:0.3268:1.17:60:658:0.8123:0.0147:0.1
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chr6 117642992 117642992 - T intronic ROS1 . . . rs11451804 . . . . . . 0.438299 0.379 . . . . . . . . . 0.4604 0.5757 0.5584 0.4433 0.4341 0.1336 0.4016 0.4516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 295 1281 chr6 117642992 . A AT 295 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1226;VD=307;AF=0.2504;SHIFT3=20;MSI=21.000;MSILEN=1;SSF=0.0169;SOR=0.82257;LSEQ=ATGCTTTCAGTATAATGGCA;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1226:307:154,153:218,169:387,307:0.2504:2,2:45.4:1:34.8:1:0.10831:1.28109:60:614:0.81:0:0.1 0/1:1281:370:206,164:200,139:339,370:0.2888:2,2:45.3:1:34.6:1:0.40332:1.14527:60:369:1:0:0.1
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chr6 117645778 117645778 - T intronic ROS1 . . . rs1053507264 . . . . . . . . . . . . . . . . . 0.0009 0.0029 0 0 0.0006 0.0003 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 170 1611 chr6 117645778 . C CT 170 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1480;VD=29;AF=0.0196;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.23359;SOR=1.26782;LSEQ=TCAAAAGCAAGGTGTTTTTG;RSEQ=TTTTTTTTGCAGAGAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1480:29:13,15:736,648:1384,29:0.0196:2,2:39.1:1:35:1:0.56735:1.31028:60:58:0.0215:0.0014:0.2 0/1:1611:25:15,9:790,723:1513,25:0.0155:2,2:44:1:35:1:0.4109:1.52:60:50:0.0167:0.0012:0
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chr6 117647255 117647260 TATATA - intronic ROS1 . . . rs61468662 . . . . . . . . . . . . . . . . . 0.1667 0.1649 0.1383 0.0957 0.1762 0.1223 0.1706 0.1597 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 245 319 chr6 117647254 . TTATATA T 245 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=306;VD=119;AF=0.3889;SHIFT3=30;MSI=18.000;MSILEN=2;SSF=0.26348;SOR=0.89012;LSEQ=TAATAGTTTGGATAATAAGA;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:119:69,50:50,55:105,119:0.3889:2,2:48.3:1:35:0:0.14053:1.52:60:238:0.3902:0:0.1 0/1:319:133:80,53:52,45:97,133:0.4169:2,2:49.6:1:34.8:1:0.34649:1.30:60:266:0.4182:0:0.1
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chr6 117657902 117657902 T G intronic ROS1 . . . rs72963572 . . . . . . 0.000199681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 305 982 chr6 117657902 . T G 305 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1034;VD=456;AF=0.441;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12597;SOR=0.89898;LSEQ=TTTTGGTTCTAGATCTTTGT;RSEQ=CCTTCCATTCTTATAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1034:456:322,134:370,206:576,456:0.441:2,2:39.7:1:34.1:1:0.03288:1.34:60:75:0.4386:0.0174:1.1 0/1:982:459:317,142:335,187:522,459:0.4674:2,2:40:1:34.5:1:0.11904:1.25:60:152:0.4658:0.0173:1.1
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chr6 117678083 117678083 A G intron ROS1 NM_002944:exon25:c.3855-5T>C . . rs2243384 ID=COSV63855476;OCCURENCE=1(breast),1(haematopoietic_and_lymphoid_tissue),3(lung) . . . . . 0.394569 0.4762 0.4254 0.4632 0.2257 0.3950 0.4565 0.4169 0.5198 0.4856 0.4738 0.4054 0.2292 0.4093 0.5033 0.4882 0.4413 0.4875 0.4189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 1 372 1763 chr6 117678083 . A G 372 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1655;VD=1648;AF=0.9958;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5579;SOR=0.93848;LSEQ=TGTCCAATACAAGCGACTAT;RSEQ=GAGGAAAAAAAAGTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1655:1648:778,870:1,0:1,1648:0.9958:0,2:41.2:1:34.7:1:0.47241:0:60:328.6:0.9976:0.0085:1.1 1/1:1763:1756:809,947:1,0:1,1756:0.996:0,2:40.8:1:34.6:1:0.46101:0:60:291.667:0.9977:0.025:1.1
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chr6 117686919 117686919 A - intron ROS1 NM_002944:exon19:c.2813-15T>- . . rs778224877 ID=COSV63858451;OCCURENCE=1(large_intestine),1(stomach) . . . . . . . . 5.313e-05 0 0.0001 0 0 4.991e-05 0.0021 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.25 142 1704 chr6 117686918 . CA C 142 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=1682;VD=15;AF=0.0089;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.44435;SOR=0.89297;LSEQ=AAGTTCCCTACAGGATGAAA;RSEQ=AAAAAAAGAAATAGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1682:15:6,9:808,858:1666,15:0.0089:2,2:41:1:35:1:0.60835:1.4123:60:30:0.0089:0.0006:0.7 0/1:1704:17:4,13:783,903:1686,17:0.01:2,2:50.2:1:34.9:1:0.08485:2.81644:60:34:0.01:0.0012:0.9
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chr6 117686943 117686943 A T intron ROS1 NM_002944:exon19:c.2813-39T>A . . rs2243383 ID=COSV63850811;OCCURENCE=3(central_nervous_system),15(soft_tissue),1(upper_aerodigestive_tract) . . . . . 0.609225 0.5863 0.5534 0.5735 0.7073 0.6289 0.6196 0.5820 0.5214 0.5488 0.6156 0.5859 0.7038 0.5837 0.4338 0.5762 0.5531 0.5287 0.5941 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 323 1412 chr6 117686943 . A T 323 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1395;VD=712;AF=0.5104;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01255;SOR=1.18769;LSEQ=AAAAGAAATAGGAGAAAAAA;RSEQ=TGGGGATTATTGACCAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1395:712:323,389:272,411:683,712:0.5104:2,2:38.1:1:34.1:1:0.03963:1.25:60:78.111:0.5076:0.0387:1.5 0/1:1412:660:251,409:319,431:750,660:0.4674:2,2:38.1:1:34.2:1:0.09188:1.20588:60:72.333:0.465:0.0305:1.5
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chr6 117708971 117708971 C T exonic ROS1 . synonymous SNV ROS1:NM_002944:exon13:c.1986G>A:p.E662E rs9489143 ID=COSV104423539;OCCURENCE=27(meninges) . . . . . 0.0644968 0.0308 0.0621 0.0653 0.0330 0.0447 0.0196 0.0537 0.0729 0.0925 0.0975 0.0493 0.0298 0.0525 0.1126 0.0222 0.0538 0.0598 0.0682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 362 2767 chr6 117708971 . C T 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2777;VD=1377;AF=0.4959;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51027;SOR=1.00006;LSEQ=AGGGTAGTACCCACTGAGGG;RSEQ=TCTGACCAGGGGCCTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2777:1377:820,557:810,581:1391,1377:0.4959:2,2:37.6:1:34.8:1:0.48704:1.06:60:458:0.4987:0.0227:1.1 0/1:2767:1372:838,534:831,559:1390,1372:0.4958:2,2:38.4:1:34.7:1:0.5083:1.06:60:342:0.4976:0.0188:1.1
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chr6 117724462 117724462 C A intron ROS1 NM_002944:exon6:c.439-22G>T . . rs2243379 ID=COSV63855806;OCCURENCE=3(central_nervous_system),1(lung),1(upper_aerodigestive_tract) . . . . . 0.669329 0.5575 0.5943 0.5510 0.8804 0.4761 0.5604 0.6086 0.4670 0.5549 0.6648 0.6222 0.8730 0.4845 0.3675 0.5440 0.5931 0.5037 0.6273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 1 385 2083 chr6 117724462 . C A 385 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2125;VD=2124;AF=0.9995;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1046;SOR=5.10882;LSEQ=TAGATCAAGGAGTGATCAAT;RSEQ=ATCAGCATTATAGAATCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2125:2124:1070,1054:0,0:0,2124:0.9995:0,2:41.7:1:34.9:1:1:0:60:1061:1:0.0198:1.8 1/1:2083:2078:1072,1006:0,0:0,2078:0.9976:0,2:42.1:1:34.9:1:1:0:60:1038:0.999:0.0043:1.8
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chr6 117725448 117725448 T G exonic ROS1 . nonsynonymous SNV ROS1:NM_002944:exon5:c.433A>C:p.T145P rs1998206 ID=COSV63854406;OCCURENCE=1(breast),1(liver),31(meninges),1(haematopoietic_and_lymphoid_tissue),1(urinary_tract),3(soft_tissue),1(lung) . . . . . 0.167732 0.1815 0.1469 0.1634 0.1616 0.1734 0.1728 0.2139 0.1474 0.1503 0.1864 0.1710 0.1571 0.1602 0.0728 0.1718 0.2195 0.1673 0.2150 0.128 0.272 T 0.000 0.629 D 0.003 0.436 P 2.045 0.562 M 0.35 0.580 T -2.17 0.490 N -0.724 0.593 T 0.210 0.570 T . . . . . 0.914 0.532 D c 0.307 0.236 0.954 0.281 0.487 0.133 0 5.41 0.782 1.607 0.362 0.964 0.580 1.000 0.715 0.113 0.194 14.627 0.681 Fibronectin type III|Immunoglobulin-like fold ENSG00000164465.14|ENSG00000164465.14|ENSG00000164465.14|ENSG00000164465.14 Adipose_Subcutaneous|Adipose_Visceral_Omentum|Lung|Thyroid 6q22.1 0.5 344 2250 chr6 117725448 . T G 344 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2377;VD=1130;AF=0.4754;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42322;SOR=0.98695;LSEQ=GGCAGCCTTTCATACCTTAG;RSEQ=ATAAGTCCAGCTTCCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2377:1130:738,392:788,457:1245,1130:0.4754:2,2:37.6:1:34:1:0.32418:1.09:60:55.5:0.4721:0.0042:1.3 0/1:2250:1077:656,421:751,418:1169,1077:0.4787:2,2:38.6:1:34.1:1:0.10636:1.15296:60:66.312:0.4764:0.0031:1.2
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chr6 117725578 117725578 T A exonic ROS1 . synonymous SNV ROS1:NM_002944:exon5:c.303A>T:p.L101L rs2243378 ID=COSV63852338;OCCURENCE=2(large_intestine),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),1(lung) . . . . . 0.67512 0.5675 0.5992 0.5539 0.8764 0.4706 0.5752 0.6202 0.4712 0.5519 0.6697 0.6261 0.8677 0.4785 0.3775 0.5655 0.6040 0.5096 0.6373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 1 398 2717 chr6 117725578 . T A 398 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2812;VD=2800;AF=0.9957;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27675;SOR=0.68911;LSEQ=GAAGCAAAGGGAGCAGTTGG;RSEQ=AGGTCTGCATTTTCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2812:2800:1423,1377:0,0:0,2800:0.9957:0,2:36.5:1:34.8:1:1:0:60:465.667:0.9975:0.0448:1.2 1/1:2717:2709:1415,1294:0,1:1,2709:0.9971:0,2:36.5:1:34.7:1:0.47786:0:60:300:0.9978:0.0438:1.2
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chr6 117730819 117730819 G A intron ROS1 NM_002944:exon4:c.229-14C>T . . rs2273601 ID=COSV63852678;OCCURENCE=1(liver),3(central_nervous_system),1(biliary_tract),1(lung),1(upper_aerodigestive_tract) . . . . . 0.360224 0.2738 0.3166 0.2811 0.4783 0.1212 0.2656 0.3035 0.2383 0.2791 0.4200 0.3241 0.4715 0.1659 0.2233 0.2706 0.2928 0.2624 0.3228 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 334 1732 chr6 117730819 . G A 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1638;VD=722;AF=0.4408;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01266;SOR=0.85465;LSEQ=ACTCCCGCTGTGGAAGACAG;RSEQ=GAGCATGACAGTCAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1638:722:332,390:422,493:915,722:0.4408:2,2:44.7:1:34.7:1:0.96022:1.00552:60:239.667:0.4422:0.0012:1.1 0/1:1732:831:344,487:420,480:900,831:0.4798:2,2:43.2:1:34.5:1:0.02927:1.23857:60:137.5:0.4825:0.0139:1.1
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chr6 117735717 117735717 A - intronic ROS1 . . . rs3836983 ID=COSV63855441;OCCURENCE=1(liver) . . . . . 0.192292 0.0883 . 0.3669 0.3430 0.3010 0.2790 0.3526 0.3878 0.3670 0.3900 0.2129 0.1614 0.125 0.1548 0.0315 0.3739 0.2443 0.2833 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 339 1774 chr6 117735716 . GA G 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1728;VD=836;AF=0.4838;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.24958;SOR=1.04915;LSEQ=CATAAGTATCATTCTGCATA;RSEQ=AAAAAAAAAAGACTACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1728:836:368,468:417,433:850,836:0.4838:2,2:45.2:1:34.9:1:0.04033:1.22459:60:1672:0.4841:0.0116:0.1 0/1:1774:837:373,464:429,454:883,837:0.4718:2,2:45:1:35:1:0.10024:1.17535:60:1674:0.4723:0.0163:0.1
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chr6 117737390 117737390 G A intron ROS1 NM_002944:exon3:c.228+31C>T . . rs2243 ID=COSV63862178;OCCURENCE=3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),1(upper_aerodigestive_tract) . . . . . 0.457069 0.4395 0.3671 0.3595 0.5597 0.2639 0.4341 0.3731 0.2879 0.3359 0.5001 0.3864 0.5467 0.2871 0.2748 0.4334 0.3598 0.3018 0.3959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q22.1 0.5 330 1400 chr6 117737390 . G A 330 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1399;VD=721;AF=0.5154;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08977;SOR=1.10995;LSEQ=TCCTCTTGAAAGAAACATCA;RSEQ=TATCAAAATAGAAATCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1399:721:481,240:441,237:678,721:0.5154:2,2:39.3:1:34.8:1:0.53489:1.08:60:359.5:0.5188:0.0157:1.1 0/1:1400:685:439,246:475,240:715,685:0.4893:2,2:39:1:34.8:1:0.36921:1.10897:60:341.5:0.4914:0.0157:1.1
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chr6 159189423 159189423 T - intronic EZR . . . rs3837013 . . . . . . 0.33766 0.1935 . . . . . . . . . 0.4163 0.3497 0.2799 0.3377 0.1399 0.4989 0.4731 0.4449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 0.5 340 1694 chr6 159189422 . GT G 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1687;VD=857;AF=0.508;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.41248;SOR=0.98257;LSEQ=TCAGCTTGTTCTTTATAGCC;RSEQ=TGTGAGAACAGCCTAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1687:857:643,214:612,218:830,857:0.508:2,2:38.8:1:34.8:1:0.57695:1.07:60:1714:0.5089:0.0539:0.1 1/0:1694:868:641,227:603,222:825,868:0.5124:2,2:40.1:1:34.9:1:0.74122:1.04:60:1736:0.5139:0.059:0.2
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chr6 159189508 159189508 G C intronic EZR . . . rs3102977 . . . . . . 0.190695 0.0129 . . . . . . . . . 0.2685 0.2836 0.1292 0.2583 0.0148 0.3270 0.2805 0.2847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 0.5 358 2756 chr6 159189508 . G C 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2818;VD=1377;AF=0.4886;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45355;SOR=0.99234;LSEQ=TAGGCAGCAGCAGCCCTGGA;RSEQ=AGCCGGGAGACACGTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2818:1377:910,467:964,471:1435,1377:0.4886:2,2:38.1:1:34.4:1:0.5486:1.05036:60:152:0.4894:0.0185:1.8 0/1:2756:1352:861,491:905,487:1392,1352:0.4906:2,2:38.5:1:34.5:1:0.47324:1.05969:60:168:0.4927:0.0174:1.8
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chr6 159189572 159189572 G A intronic EZR . . . rs901361 . . . . . . 0.0978435 0.0119 . . . . . . . . . 0.1397 0.1679 0.0632 0.1689 0.0142 0.1310 0.1429 0.1385 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 0.5 366 3003 chr6 159189572 . G A 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3090;VD=1492;AF=0.4828;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22527;SOR=0.96078;LSEQ=AGCCACAGTGGGGGAAGGAC;RSEQ=GGCCAGCGGGTCTGTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3090:1492:888,604:976,612:1588,1492:0.4828:2,2:37.8:1:34.8:1:0.28483:1.0847:60:372:0.4842:0.0123:1.6 0/1:3003:1480:912,568:917,593:1510,1480:0.4928:2,2:38.2:1:34.9:1:0.62577:1.04:60:492.333:0.4946:0.008:1.6
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chr6 159190019 159190019 T G intronic EZR . . . rs3102976 . . . . . . 0.519369 0.2054 . . . . . . . . . 0.6768 0.6012 0.4081 0.6 0.1565 0.8265 0.7552 0.7276 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 1 393 2567 chr6 159190019 . T G 393 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2566;VD=2558;AF=0.9969;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00001;SOR=4.67474;LSEQ=GGGCACATATATAATTAGAT;RSEQ=TAAAACCAGTTCCTGACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2566:2558:1614,944:0,1:1,2558:0.9969:0,2:37:1:34.8:1:0.36928:0:60:510.6:0.9984:0.0647:1.1 1/1:2567:2530:1604,926:0,0:0,2530:0.9856:0,2:37.4:1:34.7:1:1:0:60:360.429:0.9859:0.0456:1.1
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chr6 159190184 159190184 G A intronic EZR . . . rs3102975 . . . . . . 0.521565 0.2063 . . . . . . . . . 0.6792 0.6110 0.4069 0.5960 0.1553 0.8262 0.7550 0.7264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 1 401 2971 chr6 159190184 . G A 401 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2898;VD=2893;AF=0.9983;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.22563;SOR=1.75789;LSEQ=CTTTGGGGATGTCTACTTCA;RSEQ=TAGTACAGCTGGTATTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2898:2893:1592,1301:0,0:0,2893:0.9983:0,2:37:1:34.8:1:1:0:60:360.625:0.9983:0.0466:1.1 1/1:2971:2962:1706,1256:1,0:1,2962:0.997:0,2:37.7:1:34.8:1:1:0:60:492.667:0.998:0.0286:1.1
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chr6 159190800 159190800 C G intron EZR NM_001111077:exon11:c.1251+16G>C;NM_003379:exon10:c.1251+16G>C . . rs3127177 ID=COSV51910056;OCCURENCE=1(lung) . . . . . 0.182508 0.0129 0.2633 0.2247 0.2600 0.1126 0.0107 0.3400 0.2632 0.2550 0.2092 0.2590 0.2541 0.1277 0.26 0.0148 0.3213 0.2798 0.2802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 0.5 362 3000 chr6 159190800 . C G 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3045;VD=1501;AF=0.4929;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44;SOR=1.00913;LSEQ=TATAATTCAGCATCTTGAAA;RSEQ=TCAGGCCATTCCTACCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3045:1501:746,755:808,731:1539,1501:0.4929:2,2:37.5:1:34.4:1:0.12754:1.11863:60:82.389:0.4924:0.0099:1.1 0/1:3000:1472:768,704:781,745:1526,1472:0.4907:2,2:36.3:1:34.4:1:0.60884:1.04:60:85.588:0.4891:0.0223:1.1
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chr6 159191788 159191788 C T intron EZR NM_001111077:exon10:c.1090+8G>A;NM_003379:exon9:c.1090+8G>A . . rs3212308 ID=COSV61453955;OCCURENCE=2(haematopoietic_and_lymphoid_tissue) . . . . . 0.33127 0.1935 0.4257 0.4024 0.3214 0.2162 0.1481 0.4750 0.4737 0.3887 0.4319 0.4118 0.3299 0.2811 0.34 0.1406 0.5043 0.4736 0.4458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6q25.3 0.5 353 2485 chr6 159191788 . C T 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2544;VD=1238;AF=0.4866;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10286;SOR=1.07577;LSEQ=GTAGAGTGCCAGCCCCAGGG;RSEQ=GCCTGACCTCTCTCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2544:1238:602,636:661,637:1298,1238:0.4866:2,2:37.6:1:34.4:1:0.24958:1.09624:60:122.8:0.4889:0.0208:1.1 0/1:2485:1164:560,604:647,660:1307,1164:0.4684:2,2:36.9:1:34.2:1:0.49341:1.05728:60:96:0.4704:0.0237:1.1
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chr6 160113872 160113872 A G exonic SOD2 . nonsynonymous SNV SOD2:NM_000636:exon2:c.47T>C:p.V16A,SOD2:NM_001024465:exon2:c.47T>C:p.V16A,SOD2:NM_001024466:exon2:c.47T>C:p.V16A,SOD2:NM_001322814:exon2:c.47T>C:p.V16A,SOD2:NM_001322815:exon2:c.47T>C:p.V16A,SOD2:NM_001322816:exon2:c.47T>C:p.V16A rs4880 ID=COSV61622991;OCCURENCE=1(large_intestine),3(lung) 29790 SUPEROXIDE_DISMUTASE_2_POLYMORPHISM|Microvascular_complications_of_diabetes_6 .|MONDO:MONDO:0012970,MedGen:C2675128,OMIM:612634 no_assertion_criteria_provided Benign|_risk_factor 0.410743 0.125 0.4731 0.5027 0.4542 0.6497 0.1564 0.5033 0.5149 0.5081 0.5372 0.4676 0.4235 0.6062 0.5397 0.1510 0.4716 0.5131 0.5370 0.926 0.098 T 0.003 0.354 N 1 0.290 P . . . 2.8 0.179 T 0.35 0.061 N -0.931 0.440 T 0.008 0.027 T . . . . . 0.134 0.176 N c -0.854 -0.812 1.000 0.747 0.442 0.072 0 3.08 0.344 2.202 0.421 -0.259 0.088 0.649 0.279 0.004 0.083 9.062 0.354 . ENSG00000237927.1|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000112110.5|ENSG00000112110.5|ENSG00000237927.1|ENSG00000120437.7|ENSG00000112110.5|ENSG00000237927.1|ENSG00000120438.7|ENSG00000237927.1|ENSG00000112110.5|ENSG00000112110.5|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000112110.5|ENSG00000112110.5|ENSG00000112110.5|ENSG00000237927.1|ENSG00000112110.5|ENSG00000237927.1 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Tibial|Artery_Tibial|Brain_Cortex|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Transverse|Colon_Transverse|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Atrial_Appendage|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Stomach|Thyroid|Thyroid|Whole_Blood 6q25.3 0.5 364 3055 chr6 160113872 . A G 364 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3004;VD=1492;AF=0.4967;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49673;SOR=1.00174;LSEQ=TGGAGCCCAGATACCCCAAA;RSEQ=CCGGAGCCAGCTGCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3004:1492:898,594:877,622:1499,1492:0.4967:2,2:37.7:1:34.3:1:0.35228:1.07:60:73.6:0.495:0.009:1.2 0/1:3055:1516:909,607:890,643:1533,1516:0.4962:2,2:37.4:1:34.5:1:0.28589:1.08:60:167.444:0.4967:0.0232:1.2
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chr7 6013049 6013049 C G exonic PMS2 . nonsynonymous SNV PMS2:NM_001322008:exon13:c.2252G>C:p.G751A,PMS2:NM_001322010:exon13:c.2009G>C:p.G670A,PMS2:NM_001322004:exon14:c.2165G>C:p.G722A,PMS2:NM_001322006:exon14:c.2414G>C:p.G805A,PMS2:NM_001322007:exon14:c.2252G>C:p.G751A,PMS2:NM_001322013:exon14:c.1997G>C:p.G666A,PMS2:NM_000535:exon15:c.2570G>C:p.G857A,PMS2:NM_001322003:exon15:c.2165G>C:p.G722A,PMS2:NM_001322005:exon15:c.2165G>C:p.G722A,PMS2:NM_001322009:exon15:c.2198G>C:p.G733A,PMS2:NM_001322011:exon15:c.1637G>C:p.G546A,PMS2:NM_001322012:exon15:c.1637G>C:p.G546A,PMS2:NM_001322014:exon15:c.2603G>C:p.G868A,PMS2:NM_001322015:exon15:c.2261G>C:p.G754A rs1802683 ID=COSV56220850;OCCURENCE=2(breast),1(large_intestine),1(thyroid),11(upper_aerodigestive_tract) 45352 Endometrial_carcinoma|Lynch_syndrome|Lynch_syndrome_I|Hereditary_nonpolyposis_colorectal_cancer_type_4|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided Human_Phenotype_Ontology:HP:0012114,MONDO:MONDO:0002447,MedGen:C0476089,OMIM:608089,SNOMED_CT:254878006|MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0013699,MedGen:C1838333,OMIM:614337|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign . . . 0.3748 0.4289 0.4020 0.4167 0.3196 0.3585 0.3626 0.3811 0.3225 0.3920 0.3317 0.2590 0.4383 0.2642 0.2862 0.2956 0.312 0.177 T 0.000 0.629 D 0.921 0.273 P -0.32 0.035 N -1.86 0.868 D -0.79 0.219 N -1.103 0.038 T 0.000 0.001 T . . . . . 0.900 0.505 D c -0.780 -0.580 0.022 0.134 0.706 0.609 0 2.84 0.321 5.144 0.644 0.056 0.163 1.000 0.715 0.996 0.625 6.608 0.218 . . . 7p22.1 0.5 297 771 chr7 6013049 . C G 297 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=756;VD=359;AF=0.4749;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08662;SOR=0.86535;LSEQ=GTCAGTTCTGAGAAATGACA;RSEQ=CCAGGTTGGCGATGTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:359:106,253:128,267:395,359:0.4749:2,2:34.8:1:34.5:1:0.43073:1.14402:42:118.667:0.4779:0.0198:1.1 1/0:771:394:115,279:111,265:376,394:0.511:2,2:34.3:1:34.5:1:0.93702:1.01619:41:130.333:0.5104:0.0246:1.1
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chr7 6026775 6026775 T C exonic PMS2 . nonsynonymous SNV PMS2:NM_001322008:exon9:c.1303A>G:p.K435E,PMS2:NM_001322010:exon9:c.1060A>G:p.K354E,PMS2:NM_001322004:exon10:c.1216A>G:p.K406E,PMS2:NM_001322006:exon10:c.1465A>G:p.K489E,PMS2:NM_001322007:exon10:c.1303A>G:p.K435E,PMS2:NM_001322013:exon10:c.1048A>G:p.K350E,PMS2:NM_000535:exon11:c.1621A>G:p.K541E,PMS2:NM_001322003:exon11:c.1216A>G:p.K406E,PMS2:NM_001322005:exon11:c.1216A>G:p.K406E,PMS2:NM_001322009:exon11:c.1216A>G:p.K406E,PMS2:NM_001322011:exon11:c.688A>G:p.K230E,PMS2:NM_001322012:exon11:c.688A>G:p.K230E,PMS2:NM_001322014:exon11:c.1621A>G:p.K541E,PMS2:NM_001322015:exon11:c.1312A>G:p.K438E rs2228006 ID=COSV56223170;OCCURENCE=1(thyroid) 138804 Hereditary_nonpolyposis_colorectal_cancer_type_4|Mismatch_repair_cancer_syndrome_4|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified MONDO:MONDO:0013699,MedGen:C1838333,OMIM:614337|MONDO:MONDO:0030843,MedGen:C5436817,OMIM:619101|MedGen:C0009405|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.883187 0.878 0.8704 0.8511 0.9244 0.6533 0.9282 0.8432 0.8566 0.8338 0.8960 0.8722 0.9248 0.7213 0.8974 0.9202 0.8447 0.8522 0.8507 1.0 0.010 T 0.497 0.120 N 1 0.275 P -1.87 0.003 N 1.0 0.414 T 0.76 0.020 N -0.949 0.412 T 0.000 0.000 T . . . . . 0.001 0.004 N c -1.319 -1.166 0.046 0.147 0.707 0.730 0 4.66 0.577 1.502 0.351 0.014 0.141 0.009 0.180 0.013 0.120 10.569 0.442 . ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8|ENSG00000086232.8 Artery_Aorta|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cortex|Esophagus_Mucosa|Muscle_Skeletal|Nerve_Tibial|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Stomach 7p22.1 1 402 3173 chr7 6026775 . T C 402 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3121;VD=3107;AF=0.9955;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32946;SOR=0.77208;LSEQ=TGAAAAAGAGTCGTCAGTTT;RSEQ=AGGCGCTTTCTCCTGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3121:3107:1772,1335:1,0:1,3107:0.9955:0,2:39:1:34.5:1:1:0:60:123.28:0.9964:0.0186:1.1 1/1:3173:3162:1819,1343:0,2:2,3162:0.9965:0,2:37.7:1:34.6:1:0.18063:0:60:130.75:0.9968:0.0425:1.1
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chr7 6031102 6031102 A - intronic PMS2 . . . rs72363238 . . . . . . 0.332468 0.3601 . . . . . . . . . 0.3470 0.2017 0.3958 0.3993 0.3812 0.3574 0.4205 0.3713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 0.5 140 687 chr7 6031101 . TA T 140 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=693;VD=16;AF=0.0231;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.2256;SOR=1.452;LSEQ=CTTTCTCCCTTGGTTGACAT;RSEQ=AAAAAAATTACATTTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:693:16:8,8:492,184:676,16:0.0231:2,2:35.9:1:35:1:0.05204:2.6695:60:32:0.0231:0.0014:0.1 0/1:687:11:7,4:512,164:676,11:0.016:2,2:40.6:1:35:1:0.477:1.78225:60:22:0.016:0.0015:0.2
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chr7 6031169 6031169 A - intronic PMS2 . . . rs34698038 . . . . . . 0.171326 0.0923 . . . . . . . . . 0.1576 0.1492 0.1474 0.2379 0.0615 0.2831 0.1524 0.2039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 0.5 290 821 chr7 6031168 . TA T 290 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=783;VD=300;AF=0.3831;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.49171;SOR=0.99261;LSEQ=TAGAAAGCGGGAACTCTGTT;RSEQ=AAAAAAAAAAAAATTATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:783:300:175,125:243,178:421,300:0.3831:2,2:46.6:1:35:1:0.87863:1.03:60:600:0.3831:0.0102:0.1 0/1:821:316:198,118:272,181:453,316:0.3849:2,2:45.3:1:35:1:0.49881:1.12:60:632:0.3858:0.0183:0.1
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chr7 6036848 6036848 A - intronic PMS2 . . . rs879309592 . . . . . . . . . . . . . . . . . 0.0039 0.0013 0.0106 0.0160 0.0023 0.0505 0.0018 0.0187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 0.5 279 1917 chr7 6036847 . GA G 279 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1922;VD=261;AF=0.1358;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.47509;SOR=1.01041;LSEQ=AAAGCAAGACTCCGTCTCAA;RSEQ=AAAAAAAAAAAAGACACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1922:261:183,78:1119,464:1583,261:0.1358:2,2:38.5:1:34.8:1:0.88343:1.02792:60:522:0.136:0.0193:0.9 0/1:1917:258:187,71:1100,483:1583,258:0.1346:2,2:35.6:1:34.9:1:0.3424:1.16:60:516:0.1352:0.0266:0.9
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chr7 6036896 6036896 A - intronic PMS2 . . . . ID=COSV56219803;OCCURENCE=2(liver),4(large_intestine),3(stomach),1(upper_aerodigestive_tract) . . . . . . . . . . . . . . . . 6.637e-05 0 0 0 0.0006 0.0003 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 0.5 215 2301 chr7 6036895 . TA T 215 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2333;VD=68;AF=0.0291;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.33529;SOR=0.91632;LSEQ=AGCCTTAGAATCACTATCTT;RSEQ=AAAAAAAAGCTCTCAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2333:68:41,27:1304,949:2253,68:0.0291:2,2:40.9:1:35:1:0.71059:1.11:60:136:0.0292:0.0021:0.9 0/1:2301:73:47,26:1240,979:2219,73:0.0317:2,2:36.4:1:34.8:1:0.18697:1.43:60:146:0.0318:0.0052:1
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chr7 6036980 6036980 G C exonic PMS2 . synonymous SNV PMS2:NM_001322008:exon5:c.462C>G:p.S154S,PMS2:NM_001322004:exon6:c.375C>G:p.S125S,PMS2:NM_001322007:exon6:c.462C>G:p.S154S,PMS2:NM_001322010:exon6:c.375C>G:p.S125S,PMS2:NM_001322013:exon6:c.207C>G:p.S69S,PMS2:NM_000535:exon7:c.780C>G:p.S260S,PMS2:NM_001322003:exon7:c.375C>G:p.S125S,PMS2:NM_001322005:exon7:c.375C>G:p.S125S,PMS2:NM_001322006:exon7:c.780C>G:p.S260S,PMS2:NM_001322009:exon7:c.375C>G:p.S125S,PMS2:NM_001322014:exon7:c.780C>G:p.S260S,PMS2:NM_001322015:exon7:c.471C>G:p.S157S rs1805319 ID=COSV56223185;OCCURENCE=1(thyroid) 45354 Endometrial_carcinoma|Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_4|Hereditary_cancer-predisposing_syndrome|Mismatch_repair_cancer_syndrome_4|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided Human_Phenotype_Ontology:HP:0012114,MONDO:MONDO:0002447,MedGen:C0476089,OMIM:608089,SNOMED_CT:254878006|MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0013699,MedGen:C1838333,OMIM:614337|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0030843,MedGen:C5436817,OMIM:619101|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.83127 0.879 0.8238 0.8101 0.8477 0.6417 0.9263 0.7931 0.8214 0.7957 0.8172 0.8205 0.8433 0.7031 0.8444 0.9180 0.7911 0.8107 0.8010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 1 381 2217 chr7 6036980 . G C 381 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2173;VD=2165;AF=0.9963;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51676;SOR=1.10305;LSEQ=AAAAGATTATGCAGAGCATC;RSEQ=GAACAGCTCAAACCGTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2173:2165:1146,1019:0,0:0,2165:0.9963:0,2:35.7:1:34.3:1:1:0:60:85.6:0.9972:0.0479:1.1 1/1:2217:2208:1165,1043:0,1:1,2208:0.9959:0,2:36.9:1:34.3:1:0.47261:0:60:75.138:0.9973:0.0505:1.1
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chr7 6037057 6037057 - A intron PMS2 NM_000535:exon7:c.706-3->T;NM_001322008:exon5:c.388-3->T;NM_001322015:exon7:c.397-3->T;NM_001322014:exon7:c.706-3->T;NM_001322013:exon6:c.133-3->T;NM_001322012:exon7:UTR5;NM_001322011:exon7:UTR5;NM_001322005:exon7:c.301-3->T;NM_001322010:exon6:c.301-3->T;NM_001322009:exon7:c.301-3->T;NM_001322006:exon7:c.706-3->T;NM_001322007:exon6:c.388-3->T;NM_001322004:exon6:c.301-3->T;NM_001322003:exon7:c.301-3->T . . rs570998668 ID=COSV56220148;OCCURENCE=1(central_nervous_system) 195590 Lynch_syndrome|Lynch_syndrome_I|Hereditary_nonpolyposis_colorectal_cancer_type_4|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided MONDO:MONDO:0005835,MedGen:C4552100,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0013699,MedGen:C1838333,OMIM:614337|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity 0.0263578 0.0079 . 0.0381 0.0471 0.0367 0.0102 0.0321 0.0405 0.0326 0.0431 0.0961 0.1065 0.1074 0.0833 0.0350 0.0706 0.1006 0.0932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 0.5 320 1900 chr7 6037057 . G GA 320 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1930;VD=544;AF=0.2819;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.00504;SOR=0.83208;LSEQ=AGGAATGAGGCTTTGCAACT;RSEQ=AAAAAAAAAAAAAAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1930:544:289,254:425,369:794,544:0.2819:2,2:44.9:1:34.8:1:0.95549:1.01227:60:271:0.758:0:0.5 0/1:1900:609:328,281:352,314:666,609:0.3205:2,2:44.3:1:34.7:1:0.73616:1.04:60:151.25:0.9336:0:0.4
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chr7 6038621 6038621 A - intronic PMS2 . . . rs11289444 . . . . . . 0.521166 0.5228 . . . . . . . . . 0.7009 0.7155 0.6075 0.7542 0.8126 0.5606 0.7075 0.6743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p22.1 0.5 359 2280 chr7 6038620 . CA C 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2335;VD=1241;AF=0.5315;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.29291;SOR=0.96665;LSEQ=AGCAGTGCGAGACTCCCTCT;RSEQ=AAAAAAAAAAAAAAATCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2335:1241:915,326:346,123:469,1241:0.5315:2,2:44.3:1:35:1:1:1.00223:60:2482:0.5317:0.0043:0.1 1/0:2280:1231:921,310:318,114:432,1231:0.5399:2,2:45.5:1:35:1:0.6534:1.07:60:2462:0.5406:0.0044:0.1
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chr7 55214348 55214348 C T exonic EGFR . synonymous SNV EGFR:NM_001346898:exon4:c.474C>T:p.N158N,EGFR:NM_001346900:exon4:c.315C>T:p.N105N,EGFR:NM_005228:exon4:c.474C>T:p.N158N,EGFR:NM_201282:exon4:c.474C>T:p.N158N,EGFR:NM_201283:exon4:c.474C>T:p.N158N,EGFR:NM_201284:exon4:c.474C>T:p.N158N rs2072454 ID=COSV51766078;OCCURENCE=2(oesophagus),12(meninges),1(large_intestine),5(central_nervous_system),3(haematopoietic_and_lymphoid_tissue),18(soft_tissue),1(prostate),1(lung) 252899 Inflammatory_skin_and_bowel_disease,_neonatal,_2|EGFR-related_lung_cancer|not_specified|not_provided MONDO:MONDO:0014481,MedGen:C4015130,OMIM:616069|MedGen:CN130014|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.475439 0.3522 0.5151 0.5082 0.5017 0.5196 0.3746 0.4820 0.5160 0.5115 0.5527 0.5053 0.5028 0.5108 0.5497 0.3722 0.4771 0.5269 0.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.5 366 2911 chr7 55214348 . C T 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2976;VD=1460;AF=0.4906;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42785;SOR=0.98922;LSEQ=AACAACCCTGCCCTGTGCAA;RSEQ=GTGGAGAGCATCCAGTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2976:1460:783,677:837,669:1506,1460:0.4906:2,2:38.6:1:34.9:1:0.3017:1.08172:60:1459:0.4936:0.0111:1.1 0/1:2911:1436:793,643:841,628:1469,1436:0.4933:2,2:38.4:1:34.9:1:0.27817:1.08583:60:1435:0.4953:0.011:1.1
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chr7 55221655 55221655 G A intron EGFR NM_201284:exon7:c.748-49G>A;NM_001346897:exon6:c.613-49G>A;NM_201282:exon7:c.748-49G>A;NM_005228:exon7:c.748-49G>A;NM_001346898:exon7:c.748-49G>A;NM_001346899:exon6:c.613-49G>A;NM_201283:exon7:c.748-49G>A;NM_001346900:exon7:c.589-49G>A . . rs4947986 ID=COSV51773953;OCCURENCE=7(meninges),3(central_nervous_system),10(soft_tissue) 1238959 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.320687 0.6498 0.2174 0.3059 0.0943 0.3616 0.6316 0.2833 0.2773 0.2738 0.3343 0.2415 0.0998 0.3449 0.2285 0.6328 0.2869 0.2631 0.2811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.5 355 2219 chr7 55221655 . G A 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2288;VD=1198;AF=0.5236;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04541;SOR=1.10801;LSEQ=GCGCTTCCTCCGTGTGTGGC;RSEQ=CTGAGTGTACTTACCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2288:1198:778,420:704,382:1086,1198:0.5236:2,2:38.6:1:34.8:1:0.96501:1.01:60:298.5:0.5267:0.0302:1.1 0/1:2219:1105:742,363:710,397:1107,1105:0.498:2,2:38:1:34.7:1:0.13971:1.14:60:137.125:0.5002:0.0311:1.1
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chr7 55241605 55241605 C - intron EGFR NM_001346897:exon17:c.1927-9C>-;NM_001346941:exon12:c.1261-9C>-;NM_005228:exon18:c.2062-9C>-;NM_001346898:exon18:c.2062-9C>-;NM_001346899:exon17:c.1927-9C>-;NM_001346900:exon18:c.1903-9C>- . . rs776967203 ID=COSV51767406;OCCURENCE=1(bone),1(stomach),1(skin),1(large_intestine) 1028079 EGFR-related_lung_cancer MedGen:CN130014 criteria_provided,_single_submitter Uncertain_significance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.25 177 2563 chr7 55241604 . TC T 177 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3232;VD=35;AF=0.0108;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11317;SOR=1.46575;LSEQ=CCCTTGTCTCTGTGTTCTTG;RSEQ=CCCCCCAGCTTGTGGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3232:35:18,17:1905,1283:3188,35:0.0108:2,2:34.6:1:34.7:1:0.38661:1.40213:60:70:0.0109:0.0012:0.1 0/0:2563:19:16,3:1495,1045:2540,19:0.0074:2,2:38.6:1:35:0:0.03269:3.73:60:38:0.0075:0:0
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chr7 55241707 55241707 G T exonic EGFR . nonsynonymous SNV EGFR:NM_001346941:exon12:c.1354G>T:p.G452C,EGFR:NM_001346897:exon17:c.2020G>T:p.G674C,EGFR:NM_001346899:exon17:c.2020G>T:p.G674C,EGFR:NM_001346898:exon18:c.2155G>T:p.G719C,EGFR:NM_001346900:exon18:c.1996G>T:p.G666C,EGFR:NM_005228:exon18:c.2155G>T:p.G719C rs28929495 ID=COSV51766606;OCCURENCE=2(pleura),2(NS),39(lung),1(central_nervous_system) 31650 Lung_adenocarcinoma|Non-small_cell_lung_carcinoma|Glioblastoma|Nonsmall_cell_lung_cancer,_response_to_tyrosine_kinase_inhibitor_in,_somatic Human_Phenotype_Ontology:HP:0030078,MONDO:MONDO:0005061,MeSH:D000077192,MedGen:C0152013|Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MedGen:C4016032 no_assertion_criteria_provided Pathogenic/Likely_pathogenic|_drug_response . . . . . . . . . . . . . . . . . . . 0.0 0.912 D 0.000 0.843 D 1 0.810 D 3.995 0.968 H -1.23 0.789 T -7.7 0.956 D 0.740 0.937 D 0.756 0.917 D 0.561 0.960 D 0.932 0.990 0.977 0.761 D c 0.953 0.841 1.000 0.747 0.563 0.310 0 5.83 0.930 9.905 0.986 1.048 0.713 1.000 0.715 0.661 0.301 18.672 0.914 Protein kinase domain|Protein kinase, ATP binding site|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase, catalytic domain|Tyrosine-protein kinase, catalytic domain . . 7p11.2 0.25 326 2671 chr7 55241707 . G T 326 PASS STATUS=StrongSomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=4243;VD=672;AF=0.1584;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAAAAAGATCAAAGTGCTG;RSEQ=GCTCCGGTGCGTTCGGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4243:672:399,273:2198,1369:3567,672:0.1584:2,2:36.9:1:34.8:1:0.28066:1.09851:60:223:0.1604:0.0052:1.1 0/0:2671:0:0,0:1517,1152:2669,0:0:2,0:26:0:11:0:1:0:60:0:0:0:3
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chr7 55242465 55242479 GGAATTAAGAGAAGC - exonic EGFR . nonframeshift deletion EGFR:NM_001346941:exon13:c.1434_1448del:p.E479_A483del,EGFR:NM_001346897:exon18:c.2100_2114del:p.E701_A705del,EGFR:NM_001346899:exon18:c.2100_2114del:p.E701_A705del,EGFR:NM_001346898:exon19:c.2235_2249del:p.E746_A750del,EGFR:NM_001346900:exon19:c.2076_2090del:p.E693_A697del,EGFR:NM_005228:exon19:c.2235_2249del:p.E746_A750del rs121913421 ID=COSV51765119;OCCURENCE=4(salivary_gland),1(oesophagus),2(ovary),1(NS),1(stomach),1121(lung),2(thyroid),3(upper_aerodigestive_tract) 174234 Tyrosine_kinase_inhibitor_response MedGen:CN225347 no_assertion_criteria_provided drug_response . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.25 345 2290 chr7 55242464 . AGGAATTAAGAGAAGC A 345 PASS STATUS=StrongSomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3688;VD=948;AF=0.257;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAAATTCCCGTCGCTATCA;RSEQ=AACATCTCCGAAAGCCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3688:948:509,439:1529,1209:2738,948:0.257:2,2:42.6:1:34.9:1:0.25572:1.09073:60:1896:0.2594:0.0385:0.1 0/0:2290:0:0,0:1312,976:2288,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0
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chr7 55249063 55249063 G A exonic EGFR . synonymous SNV EGFR:NM_001346941:exon14:c.1560G>A:p.Q520Q,EGFR:NM_001346897:exon19:c.2226G>A:p.Q742Q,EGFR:NM_001346899:exon19:c.2226G>A:p.Q742Q,EGFR:NM_001346898:exon20:c.2361G>A:p.Q787Q,EGFR:NM_001346900:exon20:c.2202G>A:p.Q734Q,EGFR:NM_005228:exon20:c.2361G>A:p.Q787Q rs1050171 ID=COSV51769407;OCCURENCE=2(breast),15(meninges),2(biliary_tract),2(haematopoietic_and_lymphoid_tissue),11(lung) 54438 Squamous_cell_lung_carcinoma|Lung_carcinoma|Inflammatory_skin_and_bowel_disease,_neonatal,_2|EGFR-related_lung_cancer|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0005138,MedGen:C0684249|MONDO:MONDO:0014481,MedGen:C4015130,OMIM:616069|MedGen:CN130014|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.432708 0.1825 0.5424 0.5173 0.4159 0.5504 0.1599 0.4728 0.5900 0.5375 0.4979 0.5005 0.4162 0.5692 0.6589 0.1743 0.4765 0.5820 0.5245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.5 364 2786 chr7 55249063 . G A 364 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2839;VD=1421;AF=0.5005;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10057;SOR=1.07209;LSEQ=TGCCTCACCTCCACCGTGCA;RSEQ=CTCATCACGCAGCTCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2839:1421:779,642:813,594:1407,1421:0.5005:2,2:37.7:1:34.8:1:0.12009:1.12793:60:472.667:0.5037:0.0162:1.1 0/1:2786:1346:736,610:808,624:1432,1346:0.4831:2,2:39.9:1:34.6:1:0.35944:1.07317:60:148.556:0.4839:0.0072:1.1
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chr7 55266417 55266417 T C exonic EGFR . synonymous SNV EGFR:NM_001346941:exon17:c.1908T>C:p.T636T,EGFR:NM_001346897:exon22:c.2574T>C:p.T858T,EGFR:NM_001346899:exon22:c.2574T>C:p.T858T,EGFR:NM_001346898:exon23:c.2709T>C:p.T903T,EGFR:NM_001346900:exon23:c.2550T>C:p.T850T,EGFR:NM_005228:exon23:c.2709T>C:p.T903T rs1140475 ID=COSV51770428;OCCURENCE=18(meninges),3(central_nervous_system),3(lung) 1155740 Inflammatory_skin_and_bowel_disease,_neonatal,_2|EGFR-related_lung_cancer MONDO:MONDO:0014481,MedGen:C4015130,OMIM:616069|MedGen:CN130014 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.916733 0.9196 0.8891 0.8975 0.9247 0.8933 0.9284 0.8796 0.8797 0.8890 0.9370 0.8922 0.9260 0.9103 0.9139 0.9228 0.8832 0.8703 0.8878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 1 396 2988 chr7 55266417 . T C 396 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2989;VD=2977;AF=0.996;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2283;SOR=1.41944;LSEQ=TTCATCCTCTCAGGGGTGAC;RSEQ=GTTTGGGAGTTGATGACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2989:2977:1849,1128:1,1:2,2977:0.996:2,2:36.5:1:34.4:1:1:1.64:60:92.031:0.9976:0.0395:1.1 1/1:2988:2971:1854,1117:1,2:3,2971:0.9943:2,2:37.3:1:34.6:1:0.56064:3.32:60:184.688:0.997:0.0318:1.1
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chr7 55268949 55268949 A G exonic EGFR . synonymous SNV EGFR:NM_001346941:exon19:c.2214A>G:p.E738E,EGFR:NM_001346897:exon24:c.2880A>G:p.E960E,EGFR:NM_001346899:exon24:c.2880A>G:p.E960E,EGFR:NM_001346898:exon25:c.3015A>G:p.E1005E,EGFR:NM_001346900:exon25:c.2856A>G:p.E952E,EGFR:NM_005228:exon25:c.3015A>G:p.E1005E rs55737335 ID=COSV51774050;OCCURENCE=2(meninges),1(soft_tissue) 306483 EGFR-related_lung_cancer|not_provided MedGen:CN130014|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.00139776 . 0.0037 0.0022 0.0008 0.0020 0 0.0005 0.0038 0 0 0.0021 0.0008 0.0012 0.0066 0 0.0003 0.0035 0.0010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.5 363 2880 chr7 55268949 . A G 363 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2864;VD=1425;AF=0.4976;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19285;SOR=1.04827;LSEQ=CGTGCCCTGATGGATGAAGA;RSEQ=GACATGGACGACGTGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2864:1425:795,630:812,625:1437,1425:0.4976:2,2:37.9:1:34.7:1:0.7065:1.02956:60:177.125:0.4967:0.0178:1.1 0/1:2880:1399:801,598:821,652:1473,1399:0.4858:2,2:38.7:1:34.5:1:0.42918:1.06:60:115.583:0.4846:0.017:1.1
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chr7 55269063 55269064 TC - splicing EGFR NM_001346897:exon24:r.spl;NM_001346941:exon19:r.spl;NM_005228:exon25:r.spl;NM_001346898:exon25:r.spl;NM_001346899:exon24:r.spl;NM_001346900:exon25:r.spl . . rs753534663 ID=COSV51785318;OCCURENCE=1(meninges),1(bone),2(skin),1(prostate) . . . . . . . . 0.0082 0.0069 0.0073 0.0076 0.0018 0.0069 0.0074 0.0168 3.283e-05 0 0.0013 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7p11.2 0.5 228 1982 chr7 55269062 . GTC G 228 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1973;VD=90;AF=0.0456;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.45233;SOR=0.97083;LSEQ=CTCTCTGGTATGAAATCTCT;RSEQ=TCTCTCTCTCTCTCAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1973:90:34,56:805,1072:1877,90:0.0456:2,2:43.8:1:34.9:1:0.38317:1.2367:60:180:0.0458:0.0025:0.2 0/1:1982:93:35,58:786,1096:1882,93:0.0469:2,2:46.5:1:35:1:0.45244:1.18832:60:186:0.0473:0.004:0.2
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chr7 87138645 87138645 A G exonic ABCB1 . synonymous SNV ABCB1:NM_001348946:exon26:c.3435T>C:p.I1145I,ABCB1:NM_000927:exon27:c.3435T>C:p.I1145I,ABCB1:NM_001348944:exon28:c.3435T>C:p.I1145I,ABCB1:NM_001348945:exon30:c.3645T>C:p.I1215I rs1045642 ID=COSV55952233;OCCURENCE=1(stomach),1(lung) 227763 MDR1_POLYMORPHISM|Non-small_cell_lung_carcinoma|Tramadol_response|not_provided .|Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|MedGen:CN078023|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.604832 0.6022 0.5767 0.5014 0.8005 0.5471 0.6254 0.3895 0.4692 0.4769 0.3985 0.5614 0.7937 0.5382 0.6510 0.6348 0.3846 0.4651 0.4693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.12 0.5 341 2090 chr7 87138645 . A G 341 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2103;VD=1039;AF=0.4941;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47004;SOR=0.99347;LSEQ=GCCTCCTTTGCTGCCCTCAC;RSEQ=ATCTCTTCCTGTGACACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2103:1039:516,523:522,540:1062,1039:0.4941:2,2:39.6:1:34.1:1:0.82735:1.02:60:68.267:0.4907:0.0214:1.2 0/1:2090:1036:530,506:538,515:1053,1036:0.4957:2,2:38.2:1:34:1:1:1.00:60:59.941:0.4927:0.0167:1.2
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chr7 87160561 87160561 A G intron ABCB1 NM_001348946:exon21:c.2685+49T>C;NM_001348945:exon25:c.2895+49T>C;NM_000927:exon22:c.2685+49T>C;NM_001348944:exon23:c.2685+49T>C . . rs2032583 . . . . . . 0.145367 0.0694 0.1455 0.1195 0.1785 0.0979 0.0524 0.0522 0.1209 0.1171 0.1553 0.1197 0.1738 0.1038 0.15 0.0578 0.0498 0.1131 0.0927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.12 0.5 331 1580 chr7 87160561 . A G 331 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1566;VD=773;AF=0.4936;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37592;SOR=1.02542;LSEQ=GTAACAAAATAACACTGATT;RSEQ=GAATACTTTACTCTACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1566:773:519,254:535,256:791,773:0.4936:2,2:38.6:1:34.5:1:0.87145:1.02277:60:153.6:0.4923:0.0326:1.9 0/1:1580:770:517,253:564,245:809,770:0.4873:2,2:38.2:1:34.4:1:0.27892:1.12644:60:84.556:0.4847:0.0234:1.9
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chr7 87160618 87160618 A C exonic ABCB1 . nonsynonymous SNV ABCB1:NM_001348946:exon21:c.2677T>G:p.S893A,ABCB1:NM_000927:exon22:c.2677T>G:p.S893A,ABCB1:NM_001348944:exon23:c.2677T>G:p.S893A,ABCB1:NM_001348945:exon25:c.2887T>G:p.S963A rs2032582 ID=COSV55944840;OCCURENCE=1(stomach),1(urinary_tract),2(lung) 176988 Inflammatory_bowel_disease_13|Tramadol_response|not_specified|not_provided MONDO:MONDO:0012831,MedGen:C2677101,OMIM:612244|MedGen:CN078023|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.617013 0.4683 0.6781 0.5380 0.9118 0.5385 0.4628 0.4700 0.5517 0.5101 0.3500 0.6373 0.9138 0.5649 0.6391 0.5013 0.4754 0.5384 0.5459 1.0 0.010 T 0.000 0.463 N 0.999 0.216 P -1.02 0.011 N -2.24 0.872 D 1.67 0.006 N -0.903 0.477 T 0.000 0.000 T . . . . . 0.315 0.241 N c -0.825 -0.546 0.008 0.116 0.615 0.372 0 3.72 0.417 2.216 0.423 -0.466 0.054 1.000 0.715 0.985 0.512 14.563 0.676 ABC transporter type 1, transmembrane domain ENSG00000105784.11|ENSG00000085563.10 Heart_Atrial_Appendage|Testis 7q21.12 1 374 1858 chr7 87160618 . A C 374 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1853;VD=1838;AF=0.9919;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02013;SOR=0.33071;LSEQ=AGTTTGACTCACCTTCCCAG;RSEQ=ACCTTCTAGTTCTTTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1853:1838:1001,837:1,0:1,1838:0.9919:0,2:40.5:1:34.5:1:1:0:60:107.118:0.9978:0.0221:1.4 1/1:1858:1853:1054,799:0,0:0,1853:0.9973:0,2:40.7:1:34.5:1:1:0:60:108:0.9995:0.0221:1.4
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chr7 87171152 87171152 T C intronic ABCB1 . . . rs4148737 . . . . . . 0.378994 0.3006 . . . . . . . . . 0.4267 0.4461 0.4093 0.4868 0.2899 0.4270 0.4296 0.4315 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.12 0.5 355 2653 chr7 87171152 . T C 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2694;VD=1294;AF=0.4803;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00574;SOR=0.86954;LSEQ=TTTCAAACTGTCCCAAGGTG;RSEQ=CTGGGGAAAACCTGATGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2694:1294:717,577:743,651:1394,1294:0.4803:2,2:36.3:1:33.9:1:0.27812:1.09:60:34.944:0.4744:0.0271:1.1 1/0:2653:1367:749,618:713,567:1280,1367:0.5153:2,2:36.7:1:34.1:1:0.63909:1.03756:60:64.095:0.5126:0.0245:1.1
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chr7 87179601 87179601 A G exonic ABCB1 . synonymous SNV ABCB1:NM_001348946:exon12:c.1236T>C:p.G412G,ABCB1:NM_000927:exon13:c.1236T>C:p.G412G,ABCB1:NM_001348944:exon14:c.1236T>C:p.G412G,ABCB1:NM_001348945:exon16:c.1446T>C:p.G482G rs1128503 ID=COSV55946864;OCCURENCE=1(breast),1(urinary_tract),1(lung) 191350 Tramadol_response|not_specified|not_provided MedGen:CN078023|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.583866 0.373 0.6424 0.5366 0.8090 0.4948 0.3590 0.5112 0.5720 0.5029 0.3938 0.6136 0.8084 0.5334 0.6324 0.3470 0.5189 0.5594 0.5481 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.12 1 387 2608 chr7 87179601 . A G 387 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2562;VD=2540;AF=0.9914;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24253;SOR=0.75756;LSEQ=CTCTGCACCTTCAGGTTCAG;RSEQ=CCCTTCAAGATCTACCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2562:2540:1447,1093:4,3:7,2540:0.9914:2,2:37.7:1:34.2:1:1:1.00714:60:64.128:0.9948:0.0258:1.1 1/1:2608:2591:1440,1151:2,3:5,2591:0.9935:2,2:38.2:1:34.2:1:0.66102:1.88:60:73.029:0.9969:0.0272:1.1
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chr7 87180198 87180198 C T intron ABCB1 NM_001348946:exon10:c.1000-44G>A;NM_001348945:exon14:c.1210-44G>A;NM_000927:exon11:c.1000-44G>A;NM_001348944:exon12:c.1000-44G>A . . rs10276036 . 817401 Tramadol_response MedGen:CN078023 no_assertion_criteria_provided drug_response 0.567692 0.373 0.6230 0.5325 0.7565 0.4939 0.3652 0.5105 0.5730 0.5090 0.3954 0.5967 0.7492 0.5310 0.6324 0.3459 0.5186 0.5594 0.5482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.12 1 342 896 chr7 87180198 . C T 342 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=916;VD=916;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00002;SOR=0;LSEQ=TCAGGCTACTGAGATAGTGA;RSEQ=AGCAATTTTTTTTCATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:916:916:475,441:0,0:0,916:1:0,2:41.8:1:34.8:1:1:0:60:304.333:1:0.0197:1.1 1/1:896:881:457,424:0,0:0,881:0.9833:0,2:42.7:1:34.8:1:1:0:60:292.667:0.9854:0.0056:1.1
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chr7 92244422 92244422 C T UTR3 CDK6 NM_001145306:c.*32G>A;NM_001259:c.*32G>A . . rs42039 ID=COSV56004410;OCCURENCE=8(soft_tissue) 1265458 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.126997 0.0169 0.2054 0.1856 0.1032 0.1227 0.0140 0.2212 0.2533 0.2219 0.1172 0.1939 0.1075 0.1782 0.3013 0.0143 0.2176 0.2562 0.2020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.2 0.5 351 2159 chr7 92244422 . C T 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2109;VD=1017;AF=0.4822;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20799;SOR=0.94965;LSEQ=AAGCCACCAAGGGTGTTCTC;RSEQ=GCAGGATCAGCTTAAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2109:1017:679,338:714,372:1086,1017:0.4822:2,2:40.5:1:34.8:1:0.64458:1.05:60:338:0.4826:0.0152:1.1 0/1:2159:1069:722,347:729,358:1087,1069:0.4951:2,2:38.5:1:34.9:1:0.8186:1.02:60:1068:0.4979:0.0255:1.1
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chr7 92244631 92244635 ATACA - splicing CDK6 NM_001145306:exon8:r.spl;NM_001259:exon8:r.spl . . rs1610912 ID=COSV56004416;OCCURENCE=8(soft_tissue) 1242408 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.117013 0.0169 0.1878 0.1795 0.0724 0.1183 0.0133 0.2167 0.2487 0.2193 0.1159 0.1827 0.0763 0.1758 0.2933 0.0155 0.2171 0.2520 0.1994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.2 0.5 343 1887 chr7 92244630 . TATACA T 343 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1775;VD=809;AF=0.4558;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.0659;SOR=0.90299;LSEQ=AGAAAAAAATAATTGGTTGA;RSEQ=ATACATCAATGTAAATAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1775:809:303,506:401,563:964,809:0.4558:2,2:42.3:1:35:1:0.07949:1.18932:60:1618:0.4573:0.0411:0.1 0/1:1887:908:350,558:410,567:977,908:0.4812:2,2:43.9:1:35:1:0.13296:1.15274:60:1816:0.4817:0.0355:0.1
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chr7 92247333 92247333 A G intronic CDK6 . . . rs42043 . 1225607 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.174521 0.1022 . . . . . . . . . 0.2208 0.1634 0.2524 0.3046 0.1211 0.2262 0.2606 0.2149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q21.2 0.5 343 2043 chr7 92247333 . A G 343 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1997;VD=1003;AF=0.5023;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29746;SOR=1.03609;LSEQ=CCACCACCCAGTCTGGGTAG;RSEQ=GCAGGTGTCTCACTGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1997:1003:698,305:673,318:991,1003:0.5023:2,2:34.8:1:34.4:1:0.43952:1.08:60:82.583:0.5008:0.0315:1.1 0/1:2043:1008:698,310:710,324:1034,1008:0.4934:2,2:35.5:1:34.4:1:0.811:1.03:60:99.8:0.4921:0.0255:1.1
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chr7 99382096 99382096 C T upstream CYP3A4 dist=289 . . rs2740574 . 31955 CYP3A4_PROMOTER_POLYMORPHISM|Cyp3a4-v .|. no_assertion_criteria_provided Benign 0.769169 0.996 . . . . . . . . . 0.7916 0.3587 0.9211 0.9503 0.9988 0.9633 0.9621 0.9198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q22.1 1 365 1463 chr7 99382096 . C T 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1341;VD=1337;AF=0.997;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17003;SOR=2.06837;LSEQ=TCTATTAAATCGCCTCTCTC;RSEQ=TGCCCTTGTCTCTATGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1341:1337:544,793:0,0:0,1337:0.997:0,2:42.1:1:34.8:1:1:0:60:266.4:0.997:0.0134:1.1 1/1:1463:1454:583,871:1,0:1,1454:0.9938:0,2:42.1:1:34.8:1:0.40137:0:60:726:0.9966:0.0239:1.1
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chr7 116397572 116397572 A G exonic MET . synonymous SNV MET:NM_001324402:exon6:c.654A>G:p.Q218Q,MET:NM_000245:exon7:c.1944A>G:p.Q648Q,MET:NM_001127500:exon7:c.1944A>G:p.Q648Q,MET:NM_001324401:exon7:c.1944A>G:p.Q648Q rs13223756 ID=COSV59257388;OCCURENCE=1(breast),61(meninges),1(biliary_tract),3(haematopoietic_and_lymphoid_tissue),7(soft_tissue),1(lung) 99473 Renal_cell_carcinoma|Renal_cell_carcinoma,_papillary,_1|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided Human_Phenotype_Ontology:HP:0005584,Human_Phenotype_Ontology:HP:0006720,MONDO:MONDO:0005086,MeSH:D002292,MedGen:C0007134,Orphanet:ORPHA217071,SNOMED_CT:41607009|Human_Phenotype_Ontology:HP:0011797,MedGen:C1336839,OMIM:605074|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.187899 0.2728 0.1687 0.1874 0.1255 0.0754 0.3025 0.1945 0.1887 0.1855 0.2338 0.1720 0.1247 0.0993 0.2318 0.3106 0.1797 0.1835 0.2031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q31.2 0.5 354 2598 chr7 116397572 . A G 354 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2569;VD=1330;AF=0.5177;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12252;SOR=1.06848;LSEQ=AATGGCCACGGGACAACACA;RSEQ=TACAGTACATTCTCCTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2569:1330:834,496:755,479:1234,1330:0.5177:2,2:38.2:1:34.2:1:0.43933:1.07:60:65.5:0.5147:0.0191:1.1 1/0:2598:1302:802,500:793,497:1290,1302:0.5012:2,2:38.7:1:34.4:1:0.9678:1.01:60:75.588:0.4996:0.0192:1.1
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chr7 116398481 116398481 T G intron MET NM_001324401:exon9:c.2103-32T>G;NM_001127500:exon9:c.2103-32T>G;NM_001324402:exon8:c.813-32T>G;NM_000245:exon9:c.2103-32T>G . . rs73208168 . . . . . . 0.000199681 . . 9.556e-06 0 0 0 0 1.857e-05 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q31.2 0.5 346 1993 chr7 116398481 . T G 346 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2041;VD=972;AF=0.4762;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00546;SOR=0.85015;LSEQ=ATATGTGTATCTCTAATAGC;RSEQ=AAAATTCACTTCCTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2041:972:649,323:713,355:1068,972:0.4762:2,2:38.6:1:34.6:1:1:1.00:60:161:0.4749:0.0416:1.1 1/0:1993:1030:717,313:620,340:960,1030:0.5168:2,2:37.9:1:34.6:1:0.01921:1.26:60:127.75:0.5154:0.0396:1.1
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chr7 116412043 116412043 G A exonic MET . nonsynonymous SNV MET:NM_001324402:exon13:c.1738G>A:p.D580N,MET:NM_000245:exon14:c.3028G>A:p.D1010N,MET:NM_001127500:exon14:c.3082G>A:p.D1028N . ID=COSV59259218;OCCURENCE=1(NS),8(lung) 971294 Lung_carcinoma MONDO:MONDO:0005138,MedGen:C0684249 no_assertion_criteria_provided Pathogenic . . . . . . . . . . . . . . . . . . . 0.103 0.303 T 0.000 0.843 D 1 0.810 D 2.095 0.583 M -0.72 0.731 T -0.43 0.144 N -0.301 0.750 T 0.342 0.708 T . . . 0.294 0.258 0.990 0.892 D c 0.618 0.699 1.000 0.747 0.757 0.989 0 5.67 0.876 9.333 0.964 0.998 0.613 1.000 0.715 1.000 0.888 20.117 0.979 Immunoglobulin-like fold . . 7q31.2 0.25 298 2609 chr7 116412043 . G A 298 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=3006;VD=379;AF=0.1261;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=188.72153;LSEQ=ACCGAGCTACTTTTCCAGAA;RSEQ=GTATATTTCAGTTTATTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3006:379:207,172:1344,1282:2626,379:0.1261:2,2:38.7:1:34.9:1:0.22648:1.15:60:758:0.1281:0.0057:1.1 0/0:2609:2:1,1:1353,1253:2606,2:0.0008:2,2:15.5:1:35:0:1:1.07975:60:4:0.0008:0:1.5
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chr7 128846328 128846328 G C exonic SMO . synonymous SNV SMO:NM_005631:exon6:c.1164G>C:p.G388G rs2228617 ID=COSV50829466;OCCURENCE=18(meninges),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 389787 Hamartoma_of_hypothalamus|not_specified|not_provided Human_Phenotype_Ontology:HP:0002444,MONDO:MONDO:0009436,MedGen:C0342418,OMIM:241800,Orphanet:ORPHA2113,SNOMED_CT:237714006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.75619 0.7718 0.7896 0.7933 0.6949 0.7127 0.7704 0.8048 0.8364 0.7997 0.7662 0.7929 0.6895 0.7721 0.8709 0.7674 0.8099 0.8520 0.7837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q32.1 1 399 3061 chr7 128846328 . G C 399 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3118;VD=3105;AF=0.9958;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51862;SOR=0.94002;LSEQ=GATGGGGACTCTGTGAGTGG;RSEQ=ATTTGTTTTGTGGGCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3118:3105:1743,1362:0,0:0,3105:0.9958:0,2:38.9:1:34.4:1:1:0:60:118.423:0.999:0.0449:1.2 1/1:3061:3049:1707,1342:1,0:1,3049:0.9961:0,2:39.7:1:34.5:1:1:0:60:107.893:0.9977:0.0222:1.1
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chr7 128846469 128846469 A G intron SMO NM_005631:exon6:c.1264+41A>G . . rs2735842 ID=COSV50829472;OCCURENCE=16(meninges),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 1270382 Hamartoma_of_hypothalamus|not_provided Human_Phenotype_Ontology:HP:0002444,MONDO:MONDO:0009436,MedGen:C0342418,OMIM:241800,Orphanet:ORPHA2113,SNOMED_CT:237714006|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.753195 0.756 0.7895 0.7930 0.6949 0.7130 0.7621 0.8046 0.8363 0.7971 0.7678 0.7919 0.6896 0.7721 0.8709 0.7559 0.8095 0.8511 0.7816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q32.1 1 374 1801 chr7 128846469 . A G 374 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1767;VD=1765;AF=0.9989;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.3526;SOR=1.96402;LSEQ=GACCAGTTGGGCAACAAAAT;RSEQ=TACTGGGCACTTGCTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1767:1765:720,1045:0,0:0,1765:0.9989:0,2:42.6:1:34.6:1:1:0:60:219.625:0.9994:0.0034:1.2 1/1:1801:1797:743,1054:0,0:0,1797:0.9978:0,2:41.9:1:34.6:1:1:0:60:198.667:0.9978:0.0222:1.2
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chr7 140426257 140426257 A G UTR3 BRAF NM_001354609:c.*37T>C;NM_001374258:c.*37T>C . . rs3829814 . . . . . . 0.221645 0.1577 . 0.3297 0.0976 0.3718 0.1479 0.5158 0.4714 0.3563 0.2350 0.3768 0.0974 0.3055 0.4040 0.1479 0.5049 0.5340 0.4346 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q34 0.5 324 1619 chr7 140426257 . A G 324 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1463;VD=674;AF=0.4607;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.043;SOR=0.88108;LSEQ=ACAAATTGTACGAACACAAG;RSEQ=CTTAAGAAATAAGAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1463:674:443,231:483,302:785,674:0.4607:2,2:39:1:33.7:1:0.10199:1.20:60:38.647:0.4562:0.0157:1.1 0/1:1619:797:512,285:536,282:818,797:0.4923:2,2:40.7:1:33.7:1:0.60232:1.05795:60:48.812:0.489:0.0204:1.1
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chr7 140434575 140434575 A - intron BRAF NM_001354609:exon18:c.2128-5T>-;NM_001374258:exon19:c.2248-5T>-;NM_004333:exon18:c.2128-5T>-;NM_001374244:exon19:c.2248-5T>- . . rs397516899 ID=COSV56304400;OCCURENCE=1(meninges),1(upper_aerodigestive_tract) 53988 Noonan_syndrome_with_multiple_lentigines|Cardio-facio-cutaneous_syndrome|Noonan_syndrome|Noonan_syndrome_and_Noonan-related_syndrome|Rasopathy|not_specified MONDO:MONDO:0007893,MedGen:C0175704,OMIM:PS151100,Orphanet:ORPHA500|MONDO:MONDO:0015280,MedGen:C1275081,OMIM:PS115150,Orphanet:ORPHA1340,SNOMED_CT:403770008|MONDO:MONDO:0018997,MeSH:D009634,MedGen:C0028326,OMIM:PS163950,Orphanet:ORPHA648,SNOMED_CT:205824006|MONDO:MONDO:0020297,MedGen:CN260604,Orphanet:ORPHA98733|MONDO:MONDO:0021060,MedGen:CN166718,Orphanet:ORPHA536391|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . . 0.0262 0.0258 0.0248 0.0197 0.0087 0.0288 0.0273 0.0297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q34 0.5 164 290 chr7 140434574 . CA C 164 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=299;VD=22;AF=0.0736;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28699;SOR=0.80674;LSEQ=TCAATAGAGGCGAGAATCTA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:22:2,20:61,214:275,22:0.0736:2,2:28.1:1:35:1:0.18311:2.84311:60:44:0.0738:0.01:0.4 0/1:290:26:10,16:54,206:260,26:0.0897:2,2:34.2:1:35:1:0.04878:2.38:60:52:0.0897:0.0103:0.7
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chr7 140434586 140434586 G A intron BRAF NM_001354609:exon18:c.2128-16C>T;NM_001374258:exon19:c.2248-16C>T;NM_004333:exon18:c.2128-16C>T;NM_001374244:exon19:c.2248-16C>T . . rs368721021 ID=COSV56078481;OCCURENCE=12(large_intestine),1(central_nervous_system),1(biliary_tract),1(prostate),1(lung) 140238 not_specified MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign . . . 0.0043 0.0027 0.0015 0.0048 0.0005 0.0034 0.0093 0.0202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q34 0.5 58 226 chr7 140434586 . G A 58 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=SNV;DP=228;VD=3;AF=0.0132;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.49515;SOR=0.74049;LSEQ=AGAATCTACAAAAAAAAAAA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:0,3:44,164:208,3:0.0132:2,0:14.7:1:27:1:1:0:60:2:0.0127:0:2 0/1:226:4:2,2:46,160:206,4:0.0177:2,2:10.2:1:29:1:0.22488:3.45:60:3:0.0155:0:1.8
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chr7 140494073 140494073 - T intron BRAF NM_001354609:exon8:c.1140+35->A;NM_001374258:exon8:c.1140+35->A;NM_004333:exon8:c.1140+35->A;NM_001374244:exon8:c.1140+35->A . . rs759055598 ID=COSV56134929;OCCURENCE=1(liver),1(large_intestine) . . . . . . . 0.0006 0.0001 0 0.0003 0 0.0002 0.0001 0 6.35e-05 3.264e-05 0 0 0 0 0 6.71e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q34 0.5 187 1437 chr7 140494073 . G GT 187 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1434;VD=41;AF=0.0286;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.31881;SOR=1.14537;LSEQ=AAAATAAAGATACATACTTG;RSEQ=TTTTTTTTTAGTTCTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1434:41:31,9:896,353:1249,41:0.0286:2,2:37.8:1:35:1:0.47973:1.36:60:82:0.0343:0.0007:0.1 0/1:1437:36:25,11:922,334:1256,36:0.0251:2,2:36.4:1:35:1:0.571:1.21446:60:72:0.0299:0.0028:0.2
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chr7 152351282 152351282 - A intronic XRCC2 . . . rs11411109 . . . . . . . . . . . . . . . . . 0.4235 0.2955 0.4431 0.5 0.4408 0.3444 0.4863 0.4527 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q36.1 0.5 268 540 chr7 152351282 . C CA 268 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=579;VD=202;AF=0.3489;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.38189;SOR=0.95563;LSEQ=ACAGGAGTGAAACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:202:136,66:136,76:212,202:0.3489:2,2:45.8:1:35:0:0.53485:1.15:60:404:1:0:1 0/1:540:194:119,75:153,69:222,194:0.3593:2,2:44.1:1:34.9:1:0.12132:1.39636:60:388:0.9151:0:1.1
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chr7 152359603 152359603 - A intronic XRCC2 . . . rs201349111 . . . . . . . . . . . . . . . . . 0.0125 0.0211 0.0162 0.0044 0 0.0275 0.0079 0.0102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q36.1 0.5 161 1283 chr7 152359603 . G GA 161 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1391;VD=30;AF=0.0216;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.46101;SOR=1.06567;LSEQ=AACCCTTCTATATGACAAAA;RSEQ=AAAAAAAAATCTATCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1391:30:15,14:706,581:1287,30:0.0216:2,2:37.6:1:32.9:1:0.85082:1.13403:60:14:0.0234:0.0029:0.2 0/1:1283:26:17,8:659,532:1191,26:0.0203:2,2:44.1:1:34.6:1:0.22859:1.71:60:52:0.0225:0.0008:0.2
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chr7 152359651 152359651 T - intronic XRCC2 . . . rs11323323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7q36.1 0.5 284 962 chr7 152359650 . AT A 284 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1049;VD=286;AF=0.2726;SHIFT3=24;MSI=25.000;MSILEN=1;SSF=0.17997;SOR=1.10295;LSEQ=GAAAGTCACCTTTTATTTGC;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1049:286:121,165:203,200:403,286:0.2726:2,2:50:1:34.9:1:0.04394:1.38342:59:572:0.2732:0.0057:0.2 0/1:962:244:108,136:183,176:359,244:0.2536:2,2:49.3:1:34.9:1:0.11494:1.30874:59:488:0.255:0.0073:0.2
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chr8 38285914 38285916 TCA - exonic FGFR1 . nonframeshift deletion FGFR1:NM_001174066:exon3:c.129_131del:p.D44del,FGFR1:NM_001354368:exon3:c.129_131del:p.D44del,FGFR1:NM_001354370:exon3:c.129_131del:p.D44del,FGFR1:NM_023105:exon3:c.129_131del:p.D44del,FGFR1:NM_023106:exon3:c.129_131del:p.D44del,FGFR1:NM_001174063:exon4:c.396_398del:p.D133del,FGFR1:NM_001174065:exon4:c.396_398del:p.D133del,FGFR1:NM_001354367:exon4:c.396_398del:p.D133del,FGFR1:NM_001354369:exon4:c.396_398del:p.D133del,FGFR1:NM_015850:exon4:c.396_398del:p.D133del,FGFR1:NM_023110:exon4:c.396_398del:p.D133del,FGFR1:NM_001174064:exon5:c.372_374del:p.D125del,FGFR1:NM_001174067:exon5:c.495_497del:p.D166del rs138489552 ID=COSV58341980;OCCURENCE=1(large_intestine),8(stomach) 687290 Pfeiffer_syndrome|Hypogonadotropic_hypogonadism_2_with_or_without_anosmia MONDO:MONDO:0007043,MedGen:C0220658,OMIM:101600,Orphanet:ORPHA710|MONDO:MONDO:0007844,MedGen:C1563720,OMIM:147950 criteria_provided,_single_submitter Likely_benign . . 0.0148 0.0031 0.0038 0.0037 0.0032 0.0024 0.0032 0 0.0025 6.467e-05 0 0 0 0 0 0.0001 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8p11.23 0.5 207 2219 chr8 38285913 . GTCA G 207 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2221;VD=62;AF=0.0279;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.07246;SOR=1.35647;LSEQ=TCTTTCTCCTCTGAAGAGGA;RSEQ=TCATCATCATCATCATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2221:62:31,31:1130,1024:2154,62:0.0279:2,2:42.9:1:34.8:1:0.70146:1.10347:60:124:0.028:0.0014:0.1 0/1:2219:46:27,19:1144,1026:2170,46:0.0207:2,2:38.5:1:34.7:1:0.45808:1.27:60:92:0.0208:0.0027:0.2
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chr8 38286811 38286811 C G intronic FGFR1 . . . rs2304000 ID=COSV58328363;OCCURENCE=1(biliary_tract),1(haematopoietic_and_lymphoid_tissue),11(soft_tissue),2(lung) . . . . . 0.196286 0.3185 0.2032 0.2685 0.2169 0.3541 0.4015 0.2716 0.2859 0.2587 0.1353 0.1954 0.1566 0.2356 0.1623 0.3103 0.1823 0.2094 0.1605 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8p11.23 0.5 345 2145 chr8 38286811 . C G 345 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2219;VD=1093;AF=0.4926;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19789;SOR=1.05469;LSEQ=ATACCACCACCTGTTCAGGG;RSEQ=CTCTAATCACTAAGCCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2219:1093:727,366:709,412:1121,1093:0.4926:2,2:39.4:1:34.2:1:0.10921:1.15:60:77.071:0.4943:0.0126:1.1 0/1:2145:1028:688,340:741,373:1114,1028:0.4793:2,2:39.7:1:34.1:1:0.85444:1.02:60:59.471:0.4801:0.0186:1.1
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chr8 69389217 69389217 C G intronic C8orf34 . . . rs1517114 . . . . . . 0.683506 0.878 . . . . . . . . . 0.6371 0.5884 0.6711 0.5728 0.8969 0.7132 0.6176 0.6589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q13.2 1 385 2506 chr8 69389217 . C G 385 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2481;VD=2468;AF=0.9948;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36534;SOR=1.21984;LSEQ=ATGATAATTTTCCTGATAGC;RSEQ=CTTATTCCTAGAGAGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2481:2468:1427,1041:0,0:0,2468:0.9948:0,2:39.1:1:34.2:1:1:0:60:63.947:0.9979:0.0177:1.1 1/1:2506:2490:1454,1036:2,0:2,2490:0.9936:0,2:38.6:1:34.2:1:0.51401:0:60:74.455:0.9968:0.0379:1.1
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chr8 90948273 90948273 C T intronic NBN . . . rs2735384 ID=COSV55372525;OCCURENCE=11(meninges),1(large_intestine) . . . . . 0.324481 0.4206 . 0.3308 0.2826 0.5357 0.4674 . 0.3 0.3333 0.3327 0.3156 0.2611 0.2871 0.2583 0.3937 0.3209 0.3394 0.3309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 334 1533 chr8 90948273 . C T 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1540;VD=767;AF=0.4981;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21824;SOR=1.06049;LSEQ=ACAAATATGGCTGAACAACC;RSEQ=ATCTCATTTGACTAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1540:767:442,325:455,318:773,767:0.4981:2,2:39.3:1:34.9:1:0.64202:1.05201:60:766:0.5:0.0065:1.1 0/1:1533:741:426,315:467,322:789,741:0.4834:2,2:39:1:34.8:1:0.53353:1.07236:60:740:0.4862:0.0065:1.1
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chr8 90952853 90952853 - A intronic NBN . . . rs34788524 . . . . . . 0.326877 0.4117 . . . . . . . . . 0.3415 0.3078 0.3421 0.3227 0.4709 0.3399 0.3450 0.3598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 270 669 chr8 90952853 . G GA 270 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=715;VD=222;AF=0.3105;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.25;SOR=0.91909;LSEQ=AGCTACTCCATCTACTAGAG;RSEQ=AAAAAAAAAAAAAGGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:715:222:115,106:172,157:329,222:0.3105:2,2:42.5:1:34.7:1:1:1.00979:60:444:0.7708:0.021:0.1 0/1:669:220:106,113:164,175:339,220:0.3288:2,2:45.9:1:34.8:1:1:1.00:60:219:0.6887:0:0.1
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chr8 90955253 90955253 T G intronic NBN . . . rs6470524 . 1213666 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.352236 0.4663 . . . . . . . . . 0.3006 0.2215 0.3279 0.3333 0.4236 0.3238 0.3237 0.3405 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 280 786 chr8 90955253 . T G 280 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=782;VD=287;AF=0.367;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46818;SOR=0.98626;LSEQ=ATTAGGATGTAAACTGAATT;RSEQ=CTTAGGTCTCACCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:782:287:181,106:296,199:495,287:0.367:2,2:46.3:1:33.8:1:0.40287:1.15:60:27.7:0.3588:0.0038:1.6 0/1:786:291:181,110:309,186:495,291:0.3702:2,2:44:1:34.3:1:1:1.00961:60:144.5:0.37:0.0089:1.7
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chr8 90955266 90955266 - T intronic NBN . . . rs10631091 . 1254773 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . . . . . . . . . 0.3110 0.2705 0.3363 0.2910 0.4364 0.3109 0.3180 0.3422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 267 766 chr8 90955266 . C CT 267 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=755;VD=194;AF=0.257;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.27867;SOR=0.92776;LSEQ=CTGAATTTCTTAGGTCTCAC;RSEQ=TTTTTTTTTTTTTTTAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:194:110,84:231,175:406,194:0.257:2,2:51.3:1:35:0:1:1.00799:60:388:0.516:0:1.3 0/1:766:208:111,97:205,133:338,208:0.2715:2,2:46.4:1:34.8:1:0.10816:1.34618:60:416:0.6303:0.0144:1.2
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chr8 90958422 90958422 T C exonic NBN . synonymous SNV NBN:NM_002485:exon13:c.2016A>G:p.P672P,NBN:NM_001024688:exon14:c.1770A>G:p.P590P rs1061302 ID=COSV55371426;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(stomach),1(lung),9(meninges),3(large_intestine) 182835 Microcephaly,_normal_intelligence_and_immunodeficiency|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.352835 0.4673 0.2842 0.3480 0.2272 0.3457 0.4422 0.3555 0.3287 0.3847 0.4301 0.3122 0.2281 0.3394 0.3311 0.4275 0.3615 0.3328 0.3514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 332 1756 chr8 90958422 . T C 332 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1720;VD=815;AF=0.4738;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42099;SOR=0.98428;LSEQ=TAATCATCATTTATGCCAGA;RSEQ=GGATTTCTGGAAGTAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1720:815:468,347:494,409:903,815:0.4738:2,2:39:1:34:1:0.26329:1.12:60:80.5:0.4713:0.0221:1.4 0/1:1756:839:465,374:543,373:916,839:0.4778:2,2:37.9:1:34.2:1:0.11077:1.17076:60:58.929:0.4741:0.0216:1.4
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chr8 90958530 90958530 T C intron NBN NM_001024688:exon14:c.1669-7A>G;NM_002485:exon13:c.1915-7A>G . . rs2308962 ID=COSV55371846;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(skin),2(lung),9(meninges) 253192 Microcephaly,_normal_intelligence_and_immunodeficiency|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.378994 0.4673 0.3131 0.3559 0.3143 0.3486 0.4418 0.3554 0.3293 0.3873 0.4290 0.3357 0.3078 0.3484 0.34 0.4288 0.3612 0.3337 0.3589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 312 1316 chr8 90958530 . T C 312 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1276;VD=576;AF=0.4514;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23129;SOR=0.94083;LSEQ=AGTTTGTCATTGTTCTTAAA;RSEQ=GGGGTTAAGATGGATAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:576:243,333:342,355:697,576:0.4514:2,2:41:1:33.2:1:0.01515:1.31988:60:27.8:0.4437:0.0219:1.4 0/1:1316:614:275,339:350,351:701,614:0.4666:2,2:41.2:1:33.7:1:0.06782:1.22901:60:75.75:0.4644:0.0167:1.4
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chr8 90965929 90965929 A - intron NBN NM_001024688:exon12:c.1152-10T>-;NM_002485:exon11:c.1398-10T>- . . rs752561374 ID=COSV55372021;OCCURENCE=1(oesophagus),2(large_intestine) 524039 Microcephaly,_normal_intelligence_and_immunodeficiency MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009 criteria_provided,_single_submitter Likely_benign . . . 0.0008 0.0004 0.0005 0.0004 0.0011 0.0008 0 0.0013 6.675e-05 0 0.0012 0 0 0.0003 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 180 1163 chr8 90965928 . TA T 180 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1128;VD=36;AF=0.0319;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.40071;SOR=1.09465;LSEQ=TCATCCCTTTCCCTTAGATT;RSEQ=AAAAAAAAGAAGAAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1128:36:18,18:402,686:1088,36:0.0319:2,2:44.6:1:35:0:0.11776:1.71:60:72:0.032:0:0.1 0/1:1163:34:14,20:396,729:1125,34:0.0292:2,2:38.4:1:35:1:0.47161:1.29:60:68:0.0293:0.0009:0.2
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chr8 90967469 90967469 - T intron NBN NM_001024688:exon11:c.1151+42->A;NM_002485:exon10:c.1397+42->A . . rs13312923 . 1219430 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . 0.0191 0.0060 0.0600 0.0026 0.0029 0 0.0004 0.0015 0.0015 0.0182 0.0627 0.0024 0 0.0031 0 0.0002 0.0042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 203 1392 chr8 90967469 . A AT 203 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1347;VD=56;AF=0.0416;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.42972;SOR=1.05446;LSEQ=CAACAGTATAAAAAACTTTC;RSEQ=TTTTTTTTTCAGAGACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1347:56:36,20:832,326:1158,56:0.0416:2,2:44.1:1:35:0:0.22713:1.41743:60:112:0.0486:0:0.1 0/1:1392:55:35,20:843,356:1199,55:0.0395:2,2:39.5:1:35:1:0.29459:1.35281:60:110:0.046:0.0036:0.1
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chr8 90967711 90967711 A G exonic NBN . synonymous SNV NBN:NM_002485:exon10:c.1197T>C:p.D399D,NBN:NM_001024688:exon11:c.951T>C:p.D317D rs709816 ID=COSV55371961;OCCURENCE=9(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(stomach),1(lung) 182857 Microcephaly,_normal_intelligence_and_immunodeficiency|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.608626 0.6647 0.4903 0.4745 0.7693 0.5914 0.6456 0.4398 0.3681 0.4725 0.5164 0.5139 0.7626 0.5477 0.3675 0.6286 0.4433 0.3777 0.4611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 332 1710 chr8 90967711 . A G 332 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1714;VD=822;AF=0.4796;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51253;SOR=1.00022;LSEQ=GACTCCTTTACAGTGGGTGC;RSEQ=TCTTGTGAAAGCATTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1714:822:420,402:482,405:887,822:0.4796:2,2:37.5:1:34.3:1:0.1905:1.13903:60:81.2:0.4782:0.0263:1.1 0/1:1710:820:416,404:445,433:878,820:0.4795:2,2:38.6:1:34.4:1:1:1.00:60:204:0.4811:0.0205:1.1
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chr8 90970935 90970935 G A intron NBN NM_001024688:exon10:c.878+18C>T;NM_002485:exon9:c.1124+18C>T . . rs2234744 ID=COSV55373621;OCCURENCE=1(meninges),1(haematopoietic_and_lymphoid_tissue),1(lung) 196239 Microcephaly,_normal_intelligence_and_immunodeficiency|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.353035 0.4663 0.2845 0.3475 0.2264 0.3453 0.4414 0.3550 0.3284 0.3833 0.4294 0.3125 0.2273 0.3413 0.3344 0.4288 0.3617 0.3334 0.3510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 341 1835 chr8 90970935 . G A 341 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1805;VD=882;AF=0.4886;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40066;SOR=1.01907;LSEQ=AGAATAATAACAATAGTACG;RSEQ=TAATGAAGAAGCTTTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1805:882:548,334:587,333:920,882:0.4886:2,2:40.6:1:34.9:1:0.46465:1.07434:60:1764:0.4944:0.0161:1.4 0/1:1835:888:553,335:580,360:940,888:0.4839:2,2:39.8:1:34.9:1:0.80969:1.02:60:443:0.4879:0.0196:1.4
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chr8 90990479 90990479 C G exonic NBN . nonsynonymous SNV NBN:NM_002485:exon5:c.553G>C:p.E185Q,NBN:NM_001024688:exon6:c.307G>C:p.E103Q rs1805794 ID=COSV55371261;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(stomach),1(pancreas),2(lung),1(thyroid),9(meninges),1(large_intestine) 138615 Microcephaly,_normal_intelligence_and_immunodeficiency|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.357029 0.4673 0.2866 0.3482 0.2353 0.3456 0.4413 0.3549 0.3282 0.3833 0.4294 0.3143 0.2339 0.3434 0.3344 0.4289 0.3604 0.3334 0.3531 1.0 0.010 T 0.000 0.469 N 1.000 0.186 P -1.225 0.008 N 0.43 0.711 T 0.53 0.028 N -0.961 0.391 T 0.000 0.000 T . . . . . 0.086 0.143 N c -0.822 -0.550 1.000 0.432 0.732 0.924 0 3.08 0.344 2.215 0.423 -0.887 0.027 1.000 0.715 0.980 0.490 13.939 0.634 BRCT domain;SMAD/FHA domain ENSG00000104320.9|ENSG00000104320.9|ENSG00000164823.5|ENSG00000104320.9|ENSG00000104325.2|ENSG00000104320.9|ENSG00000104320.9|ENSG00000104327.3|ENSG00000104320.9|ENSG00000104320.9|ENSG00000164823.5|ENSG00000104320.9 Adipose_Subcutaneous|Artery_Tibial|Esophagus_Muscularis|Heart_Atrial_Appendage|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Testis|Thyroid|Whole_Blood|Whole_Blood 8q21.3 0.5 326 1428 chr8 90990479 . C G 326 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1366;VD=659;AF=0.4824;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36857;SOR=0.97211;LSEQ=TGGAGGCTGCTTCTTGGACT;RSEQ=AACTGCTTTCAGGAATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1366:659:363,296:398,305:703,659:0.4824:2,2:40.9:1:34.6:1:0.58528:1.064:60:130.8:0.483:0.0037:1.1 0/1:1428:699:423,276:434,294:728,699:0.4895:2,2:38.4:1:34.6:1:0.74581:1.04:60:138.8:0.4884:0.0273:1.1
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chr8 90995019 90995019 C T exonic NBN . synonymous SNV NBN:NM_002485:exon2:c.102G>A:p.L34L rs1063045 ID=COSV55371979;OCCURENCE=9(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(stomach),1(lung) 182905 Microcephaly,_normal_intelligence_and_immunodeficiency|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0009623,MedGen:C0398791,OMIM:251260,Orphanet:ORPHA647,SNOMED_CT:234638009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.379193 0.4673 0.3132 0.3555 0.3125 0.3483 0.4422 0.3553 0.3290 0.3847 0.4297 0.3349 0.3063 0.3501 0.3367 0.4271 0.3603 0.3335 0.3541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 356 2427 chr8 90995019 . C T 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2304;VD=1118;AF=0.4852;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41818;SOR=0.98638;LSEQ=ATCGACTGATCATTTTCAAT;RSEQ=AGAATGGCACAGTTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2304:1118:587,531:602,583:1185,1118:0.4852:2,2:40.6:1:34.8:1:0.42809:1.07:60:222.6:0.4873:0.0156:1.1 0/1:2427:1186:601,585:614,626:1240,1186:0.4887:2,2:39.8:1:34.9:1:0.56991:1.05:60:592:0.4915:0.0227:1.1
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chr8 90995094 90995094 T - intron NBN NM_001024688:exon2:UTR5;NM_002485:exon2:c.38-11A>- . . rs752004731 ID=COSV99620126;OCCURENCE=2(stomach) 916232 Hereditary_cancer-predisposing_syndrome MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009 criteria_provided,_single_submitter Likely_benign . . . 3.824e-05 0 0 0.0001 0 3.733e-05 0 6.136e-05 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q21.3 0.5 168 1711 chr8 90995093 . AT A 168 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1582;VD=28;AF=0.0177;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09811;SOR=1.52322;LSEQ=GTATGGTTCTCCTGAGATAA;RSEQ=TTTTTTTTAAAAAAAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1582:28:12,16:649,905:1554,28:0.0177:2,2:42.2:1:35:1:1:1.05:60:56:0.0178:0.0019:0.4 0/1:1711:20:10,10:676,1014:1690,20:0.0117:2,2:30.9:1:35:1:0.36891:1.50:60:40:0.0117:0.0012:0.5
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chr8 128750605 128750607 CAG - exonic MYC . nonframeshift deletion MYC:NM_001354870:exon2:c.139_141del:p.Q51del,MYC:NM_002467:exon2:c.142_144del:p.Q52del rs776629119 ID=COSV52368232;OCCURENCE=1(breast),1(bone),5(NS),3(large_intestine) . . . . . . . . 0.0007 0.0001 0.0004 0.0001 0.0003 0.0004 0 0.0024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8q24.21 0.5 214 3607 chr8 128750604 . CCAG C 214 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3647;VD=55;AF=0.0151;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.04807;SOR=0.73107;LSEQ=GACGAGGAGGAGAACTTCTA;RSEQ=CAGCAGCAGCAGAGCGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3647:55:35,20:2184,1406:3590,55:0.0151:2,2:34.7:1:34.8:1:0.781:1.13:60:110:0.0152:0.0022:0.2 0/1:3607:74:47,27:2070,1460:3530,74:0.0205:2,2:36.3:1:34.6:1:0.47433:1.23:60:148:0.0206:0.0036:0.2
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chr9 5073682 5073682 T - intron JAK2 NM_001322194:exon14:c.1777-16T>-;NM_001322195:exon13:c.1777-16T>-;NM_001322196:exon13:c.1777-16T>-;NM_001322199:exon14:c.562-16T>-;NM_001322198:exon14:c.562-16T>-;NM_004972:exon14:c.1777-16T>-;NM_001322204:exon11:c.1330-16T>- . . rs750624043 ID=COSV67606488;OCCURENCE=1(meninges),1(biliary_tract),1(stomach),1(upper_aerodigestive_tract) . . . . . . . 0.0187 0.0015 0.0017 0.0015 0.0009 0.0005 0.0012 0 0.0037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9p24.1 0.5 203 1701 chr9 5073681 . CT C 203 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1626;VD=51;AF=0.0314;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.4383;SOR=0.95119;LSEQ=TCAAACAACAATTCTTTGTA;RSEQ=TTTTTTTTTCCTTAGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1626:51:35,16:1017,552:1569,51:0.0314:2,2:39.3:1:34.8:1:0.65579:1.19:60:102:0.0314:0.0018:0.1 0/1:1701:56:37,19:1082,554:1636,56:0.0329:2,2:40.9:1:35:1:1:1.00293:60:112:0.033:0.0018:0.1
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chr9 5557672 5557672 T C exonic PDCD1LG2 . nonsynonymous SNV PDCD1LG2:NM_025239:exon5:c.686T>C:p.F229S rs7854303 . . . . . . 0.997804 1 0.9988 0.9992 0.9967 0.9984 1 1 0.9993 0.9986 0.9999 0.9989 0.9975 0.9964 1 1 1 0.9995 0.9980 0.552 0.065 T 0.724 0.099 N 1 0.090 P . . . 5.16 0.012 T 1.97 0.004 N -1.036 0.184 T 0.000 0.000 T . . . . . 0.001 0.005 N c -1.415 -1.354 1.000 0.747 0.707 0.730 0 0.724 0.173 -0.676 0.053 0.067 0.174 0.000 0.063 0.021 0.135 7.742 0.278 . . . 9p24.1 1 396 3019 chr9 5557672 . T C 396 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2986;VD=2962;AF=0.992;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.011;SOR=0.4102;LSEQ=GCTTCACATTTTCATCCCCT;RSEQ=CTGCATCATTGCTTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2986:2962:1665,1297:0,0:0,2962:0.992:0,2:39.3:1:34.5:1:1:0:60:97.733:0.9942:0.0171:1.1 1/1:3019:3009:1700,1309:0,1:1,3009:0.9967:0,2:40:1:34.3:1:0.43522:0:60:76.154:0.9987:0.0242:1.1
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chr9 21968199 21968199 C G UTR3 CDKN2A NM_000077:c.*29G>C;NM_001195132:c.*193G>C;NM_058197:c.*423G>C;NM_058195:c.*144G>C;NM_001363763:c.*29G>C . . rs11515 ID=COSV58682765;OCCURENCE=1(liver),1(oesophagus),17(meninges),3(central_nervous_system),22(soft_tissue) 861289 Squamous_cell_lung_carcinoma|not_specified|not_provided Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.902157 0.9812 0.8491 0.8824 0.8349 0.9323 0.9757 0.8714 0.8531 0.8588 0.9318 0.8624 0.8402 0.8831 0.8333 0.9758 0.8643 0.8625 0.8534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9p21.3 1 369 1694 chr9 21968199 . C G 369 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1714;VD=1706;AF=0.9953;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24269;SOR=1.52121;LSEQ=GACTGATGATCTAAGTTTCC;RSEQ=GAGGTTTCTCAGAGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1714:1706:1149,557:0,0:0,1706:0.9953:0,2:39.5:1:34.4:1:1:0:60:88.789:0.9959:0.0519:1.1 1/1:1694:1682:1121,561:1,0:1,1682:0.9929:0,2:38.8:1:34.4:1:1:0:60:151.909:0.9952:0.0519:1.1
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chr9 21969808 21969808 G - intronic CDKN2A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9p21.3 0.25 156 1437 chr9 21969807 . CG C 156 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1493;VD=22;AF=0.0147;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.03135;SOR=2.13366;LSEQ=CTGTAACTGGAGGGAATTGG;RSEQ=GGGGGGAGGGGAGGAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1493:22:11,11:627,841:1468,22:0.0147:2,2:37.5:1:35:0:0.52078:1.34:60:44:0.0149:0:0 0/0:1437:10:4,6:597,828:1425,10:0.007:2,2:51:1:35:0:1:1.08148:60:20:0.007:0:0
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chr9 80343587 80343587 - A intron GNAQ NM_002072:exon6:c.736-4->T . . rs397773021 ID=COSV99062273;OCCURENCE=3(central_nervous_system),4(stomach) 777831 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.372005 0.38 0.4315 0.4411 0.3760 0.4445 0.3441 0.4587 0.4642 0.4369 0.4367 0.6019 0.4886 0.5915 0.6763 0.4121 0.5959 0.6915 0.6529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q21.2 0.5 350 1846 chr9 80343587 . G GA 350 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1872;VD=1083;AF=0.5785;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.02681;SOR=1.1386;LSEQ=CTTTCCTCCATTCGGTTCTG;RSEQ=AAAAAAAAAAAAAATCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1872:1083:419,663:170,206:376,1083:0.5785:2,2:45.9:1:34.8:1:0.02822:1.30555:60:540.5:1:0:0.1 1/0:1846:1009:433,575:159,219:378,1009:0.5466:2,2:46.1:1:34.7:1:0.80738:1.04:60:335.333:1:0:0.1
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chr9 80409345 80409345 A G intron GNAQ NM_002072:exon5:c.735+34T>C . . rs1328529 ID=COSV54105959;OCCURENCE=15(meninges),3(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),3(lung),1(upper_aerodigestive_tract) 1224791 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.302915 0.2321 0.4396 0.4743 0.1408 0.4334 0.2258 0.5043 0.5791 0.4939 0.4450 0.4154 0.1569 0.4641 0.5364 0.2245 0.4845 0.5589 0.5165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q21.2 1 367 1872 chr9 80409345 . A G 367 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1893;VD=1887;AF=0.9968;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25917;SOR=0.50491;LSEQ=TACTTGTATCAGATAATAAA;RSEQ=TGATAATCCATTGCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1893:1887:1199,688:0,0:0,1887:0.9968:0,2:39.8:1:33.8:1:1:0:60:45.024:0.9973:0.0412:1.1 1/1:1872:1869:1177,692:0,0:0,1869:0.9984:0,2:39.6:1:34:1:1:0:60:45.725:0.9995:0.0337:1.1
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chr9 80646047 80646047 G A exonic GNAQ . synonymous SNV GNAQ:NM_002072:exon1:c.105C>T:p.D35D rs751518366 ID=COSV54106001;OCCURENCE=1(breast),2(liver),1(stomach),2(haematopoietic_and_lymphoid_tissue),1(skin),1(prostate),3(lung) . . . . . . . . 0.0034 0.0004 0.0185 0.0113 0.0009 0.0017 0.0085 0.0016 0.0005 0 0.0056 0 0 0.0020 0.0002 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q21.2 0.5 190 2464 chr9 80646047 . G A 190 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=2664;VD=46;AF=0.0173;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25941;SOR=1.185;LSEQ=AGCTTGAGCTCCCGGCGGGC;RSEQ=TCCCGCTTGTCCCTGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2664:46:41,5:1658,958:2616,46:0.0173:2,2:18:1:34.5:1:0.00015:4.74:38:92:0.0175:0.0034:1.2 0/1:2464:36:32,4:1516,910:2426,36:0.0146:2,2:17.4:1:35:1:0.00074:4.80:37:72:0.0148:0.0016:1.2
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chr9 86900926 86900926 G A exonic SLC28A3 . synonymous SNV SLC28A3:NM_001199633:exon13:c.1381C>T:p.L461L,SLC28A3:NM_022127:exon14:c.1381C>T:p.L461L rs7853758 ID=COSV66153362;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) 362500 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.202676 0.1558 0.1947 0.1522 0.3117 0.1995 0.1406 0.0643 0.1364 0.1333 0.1262 0.1878 0.3111 0.2029 0.2233 0.1508 0.0719 0.1488 0.1398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q21.33 0.5 361 2636 chr9 86900926 . G A 361 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2732;VD=1370;AF=0.5015;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21925;SOR=1.04479;LSEQ=GGCTGAATTCATAAAAGACA;RSEQ=CAGGGCCAGGAAGGCAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2732:1370:842,528:806,544:1350,1370:0.5015:2,2:39:1:34.7:1:0.3668:1.08:60:684:0.5042:0.0095:1.1 0/1:2636:1293:808,485:798,539:1337,1293:0.4905:2,2:37.8:1:34.8:1:0.1499:1.13:60:430:0.4918:0.0156:1.1
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chr9 87359110 87359110 - A intronic NTRK2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q21.33 0.5 162 2417 chr9 87359110 . G GA 162 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=2457;VD=26;AF=0.0106;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.53165;SOR=0.98355;LSEQ=TAAAAACTTTGACAACCCCT;RSEQ=AAAAAAAATCAGTCATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2457:26:16,9:1463,854:2317,26:0.0106:2,2:35.7:1:34.5:1:1:1.04:60:52:0.0114:0.002:0.1 0/1:2417:26:15,10:1438,839:2277,26:0.0108:2,2:39.2:1:34.6:1:0.83542:1.14256:60:52:0.0115:0.0008:0.1
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chr9 135771988 135771990 GCT - exonic TSC1 . nonframeshift deletion TSC1:NM_001162427:exon22:c.2974_2976del:p.S992del,TSC1:NM_001362177:exon22:c.2764_2766del:p.S922del,TSC1:NM_000368:exon23:c.3127_3129del:p.S1043del,TSC1:NM_001162426:exon23:c.3124_3126del:p.S1042del rs397514812 ID=COSV53767772;OCCURENCE=1(meninges),1(soft_tissue),1(thyroid),1(endometrium) 75683 Tuberous_sclerosis_1|Tuberous_sclerosis_syndrome MONDO:MONDO:0008612,MedGen:C1854465,OMIM:191100|MedGen:C0041341,OMIM:PS191100,Orphanet:ORPHA805,SNOMED_CT:7199000 criteria_provided,_single_submitter Benign . . . 0.0015 0.0015 0.0020 0.0014 0.0006 0.0015 0 0.0014 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.13 0.5 226 3321 chr9 135771987 . CGCT C 226 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3317;VD=93;AF=0.028;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.19683;SOR=1.15382;LSEQ=TTTCTCTGGGGTAGAAAGCT;RSEQ=GCTGCTGCTGCTGCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3317:93:52,41:1695,1519:3214,93:0.028:2,2:36.9:1:34.7:1:0.59877:1.14:60:186:0.0284:0.0039:0.2 0/1:3321:81:45,36:1654,1578:3232,81:0.0244:2,2:36.5:1:34.9:1:0.49982:1.19:60:162:0.0247:0.0039:0.1
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chr9 139390945 139390947 GTG - exonic NOTCH1 . nonframeshift deletion NOTCH1:NM_017617:exon34:c.7244_7246del:p.P2415del rs774361826 ID=COSV53030950;OCCURENCE=7(stomach),8(haematopoietic_and_lymphoid_tissue),1(soft_tissue),1(lung),2(large_intestine) 552442 Connective_tissue_disorder MONDO:MONDO:0003900,MedGen:C0009782 criteria_provided,_single_submitter Likely_benign . . . 0.0015 0.0013 0.0028 0.0013 0.0007 0.0015 0.0015 0.0010 3.237e-05 0 0 0 0 0 6.687e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 0.5 202 3044 chr9 139390944 . TGTG T 202 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3284;VD=56;AF=0.0171;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.3417;SOR=0.90912;LSEQ=AGCTCACGCCAAGGTGCGGC;RSEQ=GTGGTGGTGGTGGCGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3284:56:27,29:1577,1650:3227,56:0.0171:2,2:38.3:1:35:1:1:1.02655:60:112:0.0171:0.0024:0.3 0/1:3044:57:26,31:1515,1469:2984,57:0.0187:2,2:38.8:1:34.8:1:0.50427:1.22956:60:114:0.0188:0.0026:0.4
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chr9 139391636 139391636 G A exonic NOTCH1 . synonymous SNV NOTCH1:NM_017617:exon34:c.6555C>T:p.D2185D rs2229974 ID=COSV53025449;OCCURENCE=1(breast),17(meninges),1(large_intestine),3(central_nervous_system),2(skin) 270378 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified|Cardiovascular_phenotype MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374|MedGen:CN230736 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.695088 0.9494 0.5813 0.6233 0.6340 0.7362 0.9471 0.5150 0.5484 0.6020 0.6779 0.5914 0.6176 0.6734 0.5232 0.9635 0.4977 0.5569 0.5553 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 1 402 3325 chr9 139391636 . G A 402 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3310;VD=3289;AF=0.9937;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15143;SOR=0.66228;LSEQ=TCCAGCAGGCAGCCCTTGCC;RSEQ=TCCTGGGACTTCTTCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3310:3289:1764,1525:0,1:1,3289:0.9937:0,2:38:1:34.2:1:0.46383:0:60:81.225:0.9982:0.0088:1.1 1/1:3325:3311:1815,1496:0,1:1,3311:0.9958:0,2:37.3:1:34.4:1:0.45199:0:60:126.346:0.9994:0.0334:1.1
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chr9 139397707 139397707 G A exonic NOTCH1 . synonymous SNV NOTCH1:NM_017617:exon27:c.5094C>T:p.D1698D rs10521 ID=COSV53025038;OCCURENCE=1(liver),12(meninges),7(large_intestine),3(central_nervous_system),12(haematopoietic_and_lymphoid_tissue),13(soft_tissue),1(lung),4(upper_aerodigestive_tract) 370210 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified|Cardiovascular_phenotype MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374|MedGen:CN230736 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.553514 0.9018 0.4080 0.4479 0.5329 0.6068 0.8845 0.3960 0.3651 0.4223 0.3834 0.4460 0.5089 0.5240 0.3245 0.8969 0.3810 0.3772 0.3943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 1 398 2801 chr9 139397707 . G A 398 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2901;VD=2887;AF=0.9952;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.38987;SOR=1.18468;LSEQ=GCTCCCAGGAATGCGGCCAC;RSEQ=TCGGTGGCACTCTGGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2901:2887:1691,1196:1,0:1,2887:0.9952:0,2:37.8:1:34.7:1:1:0:60:205.214:0.9962:0.0355:1.1 1/1:2801:2785:1625,1160:1,0:1,2785:0.9943:0,2:38:1:34.8:1:1:0:60:308.444:0.9946:0.0296:1.1
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chr9 139400299 139400299 C A exonic NOTCH1 . nonsynonymous SNV NOTCH1:NM_017617:exon25:c.4049G>T:p.R1350L rs150343794 . 138676 Connective_tissue_disorder|Adams-Oliver_syndrome_5|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|not_specified|Cardiovascular_phenotype|not_provided MONDO:MONDO:0003900,MedGen:C0009782|MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN169374|MedGen:CN230736|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity 0.000798722 . 0.0004 0.0006 0 0 0 0.0009 0.0010 0 0.0005 0.0006 0.0003 0 0 0 0.0003 0.0011 0 0.648 0.049 T 0.005 0.329 U 0.999 0.215 N 0.955 0.240 L -2.88 0.915 D -2.08 0.475 N -0.337 0.739 T 0.595 0.855 D 0.365 0.926 D . . 0.841 0.429 D c -0.512 -0.531 0.998 0.367 0.672 0.522 0 3.83 0.431 2.089 0.411 0.054 0.162 0.967 0.338 0.003 0.074 10.480 0.437 EGF-like calcium-binding domain|EGF-like domain . . 9q34.3 0.5 355 2441 chr9 139400299 . C A 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2513;VD=1219;AF=0.4851;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04136;SOR=1.10559;LSEQ=AGCGCAGGCTGCCGCAGGTA;RSEQ=GAGCGTCATTCTCACACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2513:1219:604,615:611,678:1289,1219:0.4851:2,2:40.7:1:34.7:1:0.29869:1.09:60:202.167:0.4862:0.0135:1.4 0/1:2441:1123:585,538:652,664:1316,1123:0.4601:2,2:38.9:1:34.5:1:0.22289:1.11:60:139.375:0.4598:0.0164:1.4
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chr9 139402663 139402663 T C intron NOTCH1 NM_017617:exon20:c.3325+21A>G . . rs3124597 ID=COSV53070526;OCCURENCE=15(meninges),2(upper_aerodigestive_tract),3(central_nervous_system) 664419 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified|not_provided MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.767173 0.9137 0.6584 0.6386 0.9106 0.7227 0.8937 0.5268 0.5522 0.5836 0.6518 0.6703 0.8981 0.6683 0.6391 0.9058 0.5072 0.5567 0.5847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 1 397 2980 chr9 139402663 . T C 397 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3120;VD=3106;AF=0.9955;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0208;SOR=2.02825;LSEQ=TGATGGGCTGGGACCCGAGC;RSEQ=GGGTGGGCACAGCAGGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3120:3106:1829,1277:2,0:2,3106:0.9955:0,2:36.8:1:34.3:1:0.51573:0:60:78.641:0.9974:0.0369:1.2 1/1:2980:2953:1759,1194:3,0:3,2953:0.9909:0,2:37.3:1:34.4:1:0.27745:0:60:100.828:0.9932:0.0164:1.1
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chr9 139405261 139405261 C T intron NOTCH1 NM_017617:exon17:c.2588-4G>A . . rs3125001 ID=COSV53031458;OCCURENCE=13(meninges),3(central_nervous_system) 265345 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified|Cardiovascular_phenotype MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374|MedGen:CN230736 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.585463 0.872 0.4549 0.4760 0.6622 0.6074 0.8697 0.4727 0.3935 0.4456 0.3809 0.5007 0.6460 0.5372 0.4040 0.8807 0.4638 0.3871 0.4418 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 0.5 348 2484 chr9 139405261 . C T 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2441;VD=1190;AF=0.4875;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01819;SOR=1.12873;LSEQ=GACCTCACAGGTCTGCCCTG;RSEQ=GGGGCAGGAGGAGGCCGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2441:1190:476,714:520,726:1246,1190:0.4875:2,2:39:1:34.1:1:0.38699:1.07434:60:73.375:0.4892:0.0201:1.4 0/1:2484:1136:470,666:556,786:1342,1136:0.4573:2,2:39.8:1:33.6:1:1:1.00237:60:38.172:0.4557:0.0117:1.4
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chr9 139407932 139407932 A G exonic NOTCH1 . synonymous SNV NOTCH1:NM_017617:exon14:c.2265T>C:p.N755N rs2229971 ID=COSV53032670;OCCURENCE=9(meninges),1(large_intestine),3(central_nervous_system),1(skin) 370782 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified|Cardiovascular_phenotype MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374|MedGen:CN230736 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.527756 0.7768 0.3975 0.4039 0.6429 0.5896 0.7997 0.4357 0.3014 0.3474 0.2945 0.4428 0.6200 0.5024 0.2152 0.8152 0.4293 0.3095 0.3599 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 0.5 358 2703 chr9 139407932 . A G 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2737;VD=1349;AF=0.4929;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4591;SOR=0.99298;LSEQ=CAAGGGTTGGATTCACACTC;RSEQ=TTGTTGTTGATGTCACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2737:1349:693,656:702,679:1381,1349:0.4929:2,2:37.2:1:34.5:1:0.78875:1.02:60:191.714:0.4925:0.0183:1.1 0/1:2703:1337:675,662:696,665:1361,1337:0.4946:2,2:36.9:1:34.5:1:0.75803:1.02646:60:166.125:0.4942:0.0252:1.1
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chr9 139412197 139412197 G A intron NOTCH1 NM_017617:exon8:c.1441+7C>T . . rs9411208 ID=COSV53027880;OCCURENCE=13(meninges),3(central_nervous_system) 370791 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.696286 0.9286 0.5544 0.5834 0.7490 0.6700 0.9268 0.5810 0.4678 0.5364 0.6604 0.5928 0.7293 0.6280 0.4603 0.9273 0.5904 0.4803 0.5612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 0.5 355 2412 chr9 139412197 . G A 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2565;VD=1264;AF=0.4928;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25603;SOR=0.96193;LSEQ=TTCCCGCCCTGGCCCCGGCC;RSEQ=ACGCACCGGGCATGCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2565:1264:857,407:892,398:1290,1264:0.4928:2,2:39.9:1:34.5:1:0.46928:1.06433:60:125.4:0.4941:0.0175:1.2 1/0:2412:1212:848,364:817,370:1187,1212:0.5025:2,2:38.7:1:34.2:1:0.56467:1.05:60:74.75:0.501:0.0228:1.2
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chr9 139418260 139418260 A G exonic NOTCH1 . synonymous SNV NOTCH1:NM_017617:exon3:c.312T>C:p.N104N rs4489420 ID=COSV53027593;OCCURENCE=1(salivary_gland),13(meninges),3(central_nervous_system),2(urinary_tract) 270379 Adams-Oliver_syndrome_5|Aortic_valve_disease_1|not_specified|Cardiovascular_phenotype MONDO:MONDO:0014459,MedGen:C4014970,OMIM:616028|MONDO:MONDO:0024523,MedGen:C3887892,OMIM:109730|MedGen:CN169374|MedGen:CN230736 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.740016 0.8363 0.6087 0.6033 0.9001 0.6781 0.8574 0.6045 0.4876 0.5594 0.6627 0.6424 0.8853 0.6388 0.46 0.8547 0.6006 0.4952 0.5837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9q34.3 0.5 357 2648 chr9 139418260 . A G 357 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2706;VD=1325;AF=0.4897;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24129;SOR=0.96088;LSEQ=CAGGGGTTGGTGAGGCAGGC;RSEQ=TTGTCCAGGGGTGTCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2706:1325:822,503:862,510:1372,1325:0.4897:2,2:37.2:1:34.5:1:0.69091:1.03427:60:100.923:0.4894:0.0207:1.2 0/1:2648:1323:830,493:832,490:1322,1323:0.4996:2,2:36.2:1:34.6:1:0.93587:1.00854:60:263.6:0.5002:0.0283:1.2
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chr10 8100647 8100647 C T exonic GATA3 . synonymous SNV GATA3:NM_001002295:exon3:c.621C>T:p.A207A,GATA3:NM_002051:exon3:c.621C>T:p.A207A rs2229359 ID=COSV60519981;OCCURENCE=1(soft_tissue),1(urinary_tract),1(thyroid) 253874 Hypoparathyroidism,_deafness,_renal_disease_syndrome|not_specified MONDO:MONDO:0007797,MedGen:C1840333,OMIM:146255,Orphanet:ORPHA2237,SNOMED_CT:724282009|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.0203674 . 0.0550 0.0468 0.0114 0.0180 0.0003 0.1001 0.0708 0.0432 0.0076 0.0543 0.0137 0.0239 0.0298 0 0.0996 0.0751 0.0592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10p14 0.5 366 3193 chr10 8100647 . C T 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3360;VD=1624;AF=0.4833;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48677;SOR=1.00287;LSEQ=TCCCGTGGCAGCATGACCGC;RSEQ=CTGGGTGGAGCCTCCTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3360:1624:873,751:938,793:1731,1624:0.4833:2,2:35.9:1:34.4:1:0.80839:1.01755:60:115:0.4845:0.0167:1.2 0/1:3193:1541:785,756:872,774:1646,1541:0.4826:2,2:36.4:1:34.4:1:0.2564:1.08497:60:127.417:0.4839:0.0175:1.2
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chr10 43595968 43595968 A G exonic RET . synonymous SNV RET:NM_020630:exon2:c.135A>G:p.A45A,RET:NM_020975:exon2:c.135A>G:p.A45A rs1800858 ID=COSV60686024;OCCURENCE=1(breast),17(meninges),1(large_intestine),22(soft_tissue),1(thyroid) 174942 Pheochromocytoma|Multiple_endocrine_neoplasia,_type_2b|Multiple_endocrine_neoplasia,_type_2a|Multiple_endocrine_neoplasia,_type_2|not_specified|not_provided Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|MONDO:MONDO:0008082,MeSH:D018814,MedGen:C0025269,OMIM:162300,Orphanet:ORPHA247709,SNOMED_CT:6153000,SNOMED_CT:61530001|MONDO:MONDO:0008234,MeSH:D018813,MedGen:C0025268,OMIM:171400,Orphanet:ORPHA247698,SNOMED_CT:61808009|MONDO:MONDO:0019003,MedGen:C4048306,Orphanet:ORPHA653,SNOMED_CT:61808009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.753594 0.5268 0.8092 0.7359 0.9528 0.7540 0.5525 0.6424 0.7355 0.7205 0.7309 0.7726 0.9506 0.7787 0.6656 0.5790 0.6447 0.7260 0.7041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 392 2752 chr10 43595968 . A G 392 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2753;VD=2732;AF=0.9924;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32824;SOR=1.19262;LSEQ=AAGCTGTATGTGGACCAGGC;RSEQ=GCCGGCACGCCCTTGCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2753:2732:1598,1134:1,1:2,2732:0.9924:2,2:38.8:1:34.4:1:1:1.41:60:104.077:0.9952:0.0265:1.1 1/1:2752:2727:1610,1117:0,3:3,2727:0.9909:0,2:38.4:1:34.5:1:0.06894:0:60:169.438:0.996:0.0291:1.1
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chr10 43604950 43604950 A G intronic RET . . . rs1864403 ID=COSV60686033;OCCURENCE=22(soft_tissue) 1272386 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.754193 0.5198 . . . . . . . . . 0.7729 0.9488 0.7792 0.6755 0.5774 0.6494 0.7265 0.7041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 402 3102 chr10 43604950 . A G 402 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3030;VD=3017;AF=0.9957;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47631;SOR=0.90129;LSEQ=TTCAAAAATGCAAGAGCAAT;RSEQ=CTGGGTAAATCTGCATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3030:3017:1697,1320:2,1:3,3017:0.9957:2,2:38.9:1:34.5:1:1:1.55547:60:166.611:0.9957:0.0142:1.1 1/1:3102:3090:1800,1290:1,2:3,3090:0.9961:2,2:39.4:1:34.7:1:0.57494:2.79:60:308:0.9968:0.0148:1.1
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chr10 43605392 43605392 G A intronic RET . . . rs2251674 ID=COSV60686041;OCCURENCE=22(soft_tissue) . . . . . 0.72484 0.5188 . . . . . . . . . 0.7456 0.8580 0.7745 0.6755 0.5737 0.6429 0.7254 0.6973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 400 3048 chr10 43605392 . G A 400 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2983;VD=2974;AF=0.997;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04872;SOR=2.07253;LSEQ=CACGCATGTTCTCGCATGCC;RSEQ=CTCTCCCTTGCAGAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2983:2974:1728,1246:2,1:3,2974:0.997:2,2:38.6:1:34.4:1:1:1.44196:60:101.552:0.998:0.0208:1.1 1/1:3048:3029:1711,1318:2,3:5,3029:0.9938:2,2:38.8:1:34.6:1:0.65854:1.95:60:150.45:0.997:0.039:1.1
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chr10 43605611 43605617 GTCTCAT TCTCATG intronic RET . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 0.5 243 2962 chr10 43605611 . GTCTCAT TCTCATG 243 p8 STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Complex;DP=3254;VD=138;AF=0.0424;SHIFT3=6;MSI=4.000;MSILEN=1;SSF=0.51467;SOR=0.99682;LSEQ=GCGACAAGACAGAGGGCCCC;RSEQ=GGGGGGCGGGGCAAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3254:138:87,51:1843,1253:3096,138:0.0424:2,2:7.4:1:34.2:1:0.42618:1.16:60:276:0.0429:0.0403:0.2 0/1:2962:126:86,40:1692,1127:2819,126:0.0425:2,2:7:1:34.1:1:0.07656:1.43:60:62:0.0424:0.0412:0.3
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chr10 43605617 43605617 - G intronic RET . . . rs397725440 ID=COSV60686045;OCCURENCE=3(soft_tissue) . . . . . 0.105431 0.12 . . . . . . . . . 0.0767 0.0841 0.0430 0.0927 0.1150 0.0736 0.0705 0.0777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 0.5 358 2720 chr10 43605617 . T TG 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=2992;VD=1328;AF=0.4439;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.44697;SOR=0.99151;LSEQ=GAGGGCCCCGGGGGGTCTCA;RSEQ=GGGGGGCGGGGCAAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2992:1328:755,573:937,643:1580,1328:0.4439:2,2:40:1:34.6:1:0.18668:1.10591:60:165:0.8402:0.0107:0.2 0/1:2720:1213:721,491:847,588:1435,1213:0.446:2,2:40.3:1:34.5:1:0.81188:1.02:60:133.667:0.8448:0.0085:0.2
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chr10 43605860 43605860 T G intronic RET . . . rs1864402 ID=COSV60686051;OCCURENCE=22(soft_tissue) . . . . . 0.742412 0.5317 . . . . . . . . . 0.7599 0.9029 0.7769 0.6767 0.5978 0.6426 0.7258 0.7029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 404 3068 chr10 43605860 . T G 404 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3295;VD=3207;AF=0.9733;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1671;LSEQ=CTGGTTTTTGCTGTGGTCAC;RSEQ=TGTGGGCCTGGGAGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3295:3207:1834,1373:0,0:0,3207:0.9733:0,2:38.6:1:34.7:1:1:0:60:319.7:0.9759:0.0173:1.8 1/1:3068:3054:1864,1190:0,0:0,3054:0.9954:0,2:38.5:1:34.7:1:1:0:60:217.143:0.9984:0.0297:1.8
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chr10 43605902 43605902 A G intronic RET . . . rs1864401 ID=COSV60686055;OCCURENCE=22(soft_tissue) . . . . . 0.743011 0.5327 . . . . . . . . . 0.7603 0.9015 0.7799 0.6755 0.5972 0.6460 0.7263 0.7100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 398 2880 chr10 43605902 . A G 398 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3175;VD=3163;AF=0.9962;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0878;SOR=1.75029;LSEQ=CCCTGCTCTGGCCCGCCCCC;RSEQ=TCTCGCCATCTGTGGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3175:3163:1741,1422:1,4:5,3163:0.9962:2,2:36.7:1:34.3:1:0.1813:4.90:60:94.848:0.9975:0.0306:1.8 1/1:2880:2861:1641,1220:1,0:1,2861:0.9934:0,2:37.5:1:34.4:1:1:0:60:101.179:0.9979:0:1.8
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chr10 43607221 43607221 C G intronic RET . . . rs3026748 ID=COSV60687535;OCCURENCE=8(soft_tissue) 1251481 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0175719 . . . . . . . . . . 0.0328 0.0081 0.0227 0.0166 0.0006 0.0584 0.0449 0.0439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 0.5 365 3200 chr10 43607221 . C G 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3241;VD=1542;AF=0.4758;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11173;SOR=0.93994;LSEQ=CATGCCCTCTTAGGAACATG;RSEQ=TGACACAGCTGCCATTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3241:1542:937,605:1011,681:1692,1542:0.4758:2,2:39.8:1:34.5:1:0.56507:1.04:60:153.2:0.4759:0.0077:1.1 0/1:3200:1572:957,615:966,655:1621,1572:0.4913:2,2:38.4:1:34.4:1:0.4696:1.06:60:86.333:0.491:0.0228:1.1
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chr10 43607756 43607756 G A intronic RET . . . rs3026750 . . . . . . 0.701677 0.496 . . . . . . . . . 0.7643 0.8353 0.7823 0.7433 0.5280 0.7655 0.7497 0.7335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 402 3200 chr10 43607756 . G A 402 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3298;VD=3172;AF=0.9618;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24466;SOR=1.10024;LSEQ=TGGGGCCCTGCCAGCCTGGG;RSEQ=TGGCTCTCCCTGCTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3298:3172:1943,1229:2,0:2,3172:0.9618:0,2:39.6:1:34.6:1:0.52529:0:60:150.048:0.9645:0:1.1 1/1:3200:3066:1917,1149:2,0:2,3066:0.9581:0,2:39.5:1:34.6:1:0.53134:0:60:138.364:0.9593:0:1.1
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chr10 43607760 43607760 C - intronic RET . . . rs34827976 . . . . . . 0.70008 0.4911 . . . . . . . . . 0.7642 0.8353 0.7823 0.7433 0.5287 0.7655 0.7493 0.7335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 406 3281 chr10 43607759 . GC G 406 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=3158;VD=3149;AF=0.9972;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53367;SOR=1.06969;LSEQ=GGCCCTGCCAGCCTGGGGTG;RSEQ=TCTCCCTGCTCCAGGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3158:3149:1928,1221:1,1:2,3149:0.9972:2,2:40:1:34.8:1:1:1.58:60:3148:0.9997:0.0545:1.1 1/1:3281:3271:2034,1237:0,0:0,3271:0.997:0,2:37.6:1:34.8:1:1:0:60:1634.5:0.9994:0.1192:1.1
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chr10 43610366 43610366 G A intronic RET . . . rs1864400 ID=COSV60687565;OCCURENCE=2(large_intestine) 1214761 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.7498 0.4742 . . . . . . . . . 0.8143 0.9094 0.8115 0.7914 0.5405 0.7994 0.7951 0.7735 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 406 3324 chr10 43610366 . G A 406 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3308;VD=3302;AF=0.9982;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3987;SOR=1.32764;LSEQ=ACAGTCTGTGGGGTGGGACT;RSEQ=TGATGAGGTGCCGTTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3308:3302:1996,1306:1,0:1,3302:0.9982:0,2:38.1:1:34.8:1:1:0:60:1650:0.9982:0.0118:1.6 1/1:3324:3316:2074,1242:1,0:1,3316:0.9976:0,2:37.2:1:34.8:1:1:0:60:367.444:0.9976:0.0418:1.6
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chr10 43610455 43610455 T C intronic RET . . . rs1864399 . 1250324 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.717851 0.4871 . . . . . . . . . 0.7822 0.8892 0.7888 0.7483 0.5442 0.7656 0.7523 0.7392 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 402 3322 chr10 43610455 . T C 402 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3418;VD=3403;AF=0.9956;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30335;SOR=0.75374;LSEQ=CAGTGTGGATGGAGGGGCAC;RSEQ=GAAGTCAGAAGGGGGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3418:3403:1972,1431:1,2:3,3403:0.9956:2,2:37.1:1:34.3:1:0.57631:2.76:60:90.973:0.9979:0.05:1.8 1/1:3322:3311:1984,1327:2,0:2,3311:0.9967:0,2:37.8:1:34.4:1:0.51964:0:60:136.958:0.9988:0.0512:1.8
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chr10 43610558 43610558 C T intronic RET . . . rs2742233 . . . . . . 0.71246 0.4742 . . . . . . . . . 0.7797 0.8828 0.7876 0.7483 0.5391 0.7659 0.7520 0.7347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 403 3102 chr10 43610558 . C T 403 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2978;VD=2962;AF=0.9946;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47949;SOR=1.08045;LSEQ=ATCCTGGAGCCTCCTTGTCC;RSEQ=GGCCAGGCAGGCCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2978:2962:1531,1431:0,1:1,2962:0.9946:0,2:38.7:1:34.8:1:0.48329:0:60:739.5:0.9963:0:1.4 1/1:3102:3084:1670,1414:2,1:3,3084:0.9942:2,2:36.8:1:34.8:1:1:1.69313:60:439.571:0.9968:0.0532:1.4
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chr10 43611708 43611708 A G intronic RET . . . rs741968 . 1257744 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.752995 0.4742 . . . . . . . . . 0.8220 0.9157 0.8138 0.7914 0.5377 0.8102 0.8049 0.7796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 398 2901 chr10 43611708 . A G 398 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3034;VD=3016;AF=0.9941;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48422;SOR=0.92923;LSEQ=TGGACACTTCCACTGTAGTC;RSEQ=GAGGTCCTGGGCTGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3034:3016:1786,1230:3,1:4,3016:0.9941:2,2:36.8:1:34.5:1:0.64995:2.06561:60:166.556:0.9963:0.0531:1.1 1/1:2901:2885:1671,1214:4,1:5,2885:0.9945:2,2:37:1:34.5:1:0.40588:2.90508:60:114.4:0.9951:0.0414:1.1
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chr10 43611865 43611865 T C intronic RET . . . rs2256550 ID=COSV60688429;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(skin),3(lung) 665137 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.469449 0.256 . . . . . . . . . 0.5585 0.6646 0.4354 0.5199 0.3123 0.5117 0.5449 0.5113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 403 3119 chr10 43611865 . T C 403 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3225;VD=3217;AF=0.9975;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00258;SOR=3.11786;LSEQ=GGGGCCTGGCTGTGGGGTCC;RSEQ=GCCCAGGGCAGAGACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3225:3217:1957,1260:4,0:4,3217:0.9975:0,2:37.7:1:34.6:1:0.16057:0:60:133.042:0.9981:0.0112:1.1 1/1:3119:3095:1857,1238:4,3:7,3095:0.9923:2,2:37.3:1:34.5:1:1:1.12:60:161.895:0.9958:0.0135:1.1
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chr10 43612226 43612226 C T intron RET NM_020630:exon12:c.2284+47C>T;NM_020975:exon12:c.2284+47C>T;NM_001355216:exon9:c.1522+47C>T . . rs760466 ID=COSV60689537;OCCURENCE=12(soft_tissue) 253767 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.120607 0.0546 0.2037 0.2103 0.0519 0.1940 0.0634 0.2037 0.2812 0.1941 0.1426 0.1874 0.0549 0.2192 0.2585 0.0580 0.2073 0.2701 0.2179 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 0.5 257 1349 chr10 43612226 . C T 257 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1444;VD=611;AF=0.4231;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.2394;SOR=1.059;LSEQ=CCCTGGGGGAGTCTCCGGGG;RSEQ=GGGGGGCGGGTGAGGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1444:611:285,326:321,490:811,611:0.4231:2,2:40.1:1:27.8:1:0.00799:1.33:60:3.629:0.4144:0.0083:1.3 0/1:1349:552:272,280:304,474:778,552:0.4092:2,2:39.9:1:28.6:1:0.00026:1.51:60:4.159:0.4027:0.0089:1.3
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chr10 43613843 43613843 G T exonic RET . synonymous SNV RET:NM_001355216:exon10:c.1545G>T:p.L515L,RET:NM_020630:exon13:c.2307G>T:p.L769L,RET:NM_020975:exon13:c.2307G>T:p.L769L rs1800861 ID=COSV60687116;OCCURENCE=1(breast),17(meninges),3(biliary_tract),1(stomach),1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),3(lung) 175112 Pheochromocytoma|Multiple_endocrine_neoplasia,_type_2b|Multiple_endocrine_neoplasia,_type_2a|Multiple_endocrine_neoplasia,_type_2|not_specified|not_provided Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|MONDO:MONDO:0008082,MeSH:D018814,MedGen:C0025269,OMIM:162300,Orphanet:ORPHA247709,SNOMED_CT:6153000,SNOMED_CT:61530001|MONDO:MONDO:0008234,MeSH:D018813,MedGen:C0025268,OMIM:171400,Orphanet:ORPHA247698,SNOMED_CT:61808009|MONDO:MONDO:0019003,MedGen:C4048306,Orphanet:ORPHA653,SNOMED_CT:61808009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.71246 0.4742 0.8026 0.7408 0.8844 0.7672 0.5040 0.7693 0.7723 0.7253 0.6418 0.7799 0.8831 0.7888 0.7333 0.5354 0.7661 0.7524 0.7403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 390 2310 chr10 43613843 . G T 390 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2434;VD=2420;AF=0.9942;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1723;SOR=0.60079;LSEQ=AACGCCTCCCCGAGTGAGCT;RSEQ=CGAGACCTGCTGTCAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2434:2420:1499,921:0,0:0,2420:0.9942:0,2:41.2:1:34.7:1:1:0:60:200.667:0.9971:0.0058:1.1 1/1:2310:2302:1362,940:0,0:0,2302:0.9965:0,2:40.2:1:34.6:1:1:0:60:163.429:0.9974:0.0372:1.2
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chr10 43615505 43615505 G A intron RET NM_020630:exon15:c.2608-24G>A;NM_020975:exon15:c.2608-24G>A;NM_001355216:exon12:c.1846-24G>A . . rs2472737 ID=COSV60686346;OCCURENCE=1(biliary_tract),3(lung) 36297 Multiple_endocrine_neoplasia,_type_2|not_specified|not_provided MONDO:MONDO:0019003,MedGen:C4048306,Orphanet:ORPHA653,SNOMED_CT:61808009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.173123 0.1974 0.1977 0.2130 0.1604 0.1517 0.2386 0.3047 0.2329 0.2175 0.1682 0.2082 0.1498 0.1623 0.1812 0.2466 0.2759 0.2231 0.2429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 0.5 365 2863 chr10 43615505 . G A 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2959;VD=1416;AF=0.4785;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46858;SOR=0.9945;LSEQ=CTGCCTGGCCATGGCCTGAC;RSEQ=ACTCGTGCTATTTTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2959:1416:892,524:934,606:1540,1416:0.4785:2,2:39.5:1:34.9:1:0.19778:1.10:60:1415:0.4808:0.0108:1.1 0/1:2863:1374:875,499:926,556:1482,1374:0.4799:2,2:40.7:1:34.8:1:0.5098:1.05:60:342.5:0.4819:0.0108:1.1
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chr10 43622217 43622217 T C intron RET NM_020975:exon19:c.3187+47T>C . . rs2075912 ID=COSV60689472;OCCURENCE=1(breast),18(meninges),1(biliary_tract) 174666 Pheochromocytoma|Multiple_endocrine_neoplasia,_type_2b|Multiple_endocrine_neoplasia,_type_2a|Multiple_endocrine_neoplasia,_type_2|not_specified Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|MONDO:MONDO:0008082,MeSH:D018814,MedGen:C0025269,OMIM:162300,Orphanet:ORPHA247709,SNOMED_CT:6153000,SNOMED_CT:61530001|MONDO:MONDO:0008234,MeSH:D018813,MedGen:C0025268,OMIM:171400,Orphanet:ORPHA247698,SNOMED_CT:61808009|MONDO:MONDO:0019003,MedGen:C4048306,Orphanet:ORPHA653,SNOMED_CT:61808009|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.754992 0.4762 0.8533 0.8031 0.9188 0.8026 0.5426 0.8167 0.8331 0.7958 0.7455 0.8233 0.9165 0.8138 0.7781 0.5378 0.8112 0.8068 0.7806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q11.21 1 309 550 chr10 43622217 . T C 309 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=500;VD=498;AF=0.996;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17708;SOR=2.74375;LSEQ=TTCTAGCACCGCTGTCCCCT;RSEQ=TGCACTATCCTTCCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:500:498:137,361:0,0:0,498:0.996:0,2:38:1:34.3:1:1:0:60:82:0.996:0.036:1.1 1/1:550:544:127,417:0,0:0,544:0.9891:0,2:39.1:1:34.1:1:1:0:60:89.667:0.9908:0.0364:1.1
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chr10 88646586 88646586 T - intronic BMPR1A . . . rs10572910 ID=COSV63135254;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) . . . . . 0.514577 0.6379 . . . . . . . . . 0.5708 0.3929 0.6329 0.5882 0.7587 0.2157 0.6757 0.6176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.2 0.5 299 1079 chr10 88646585 . CT C 299 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1080;VD=392;AF=0.363;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.36588;SOR=1.0354;LSEQ=AACACCTCCGTATTTTGTCA;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1080:392:193,199:152,164:316,392:0.363:2,2:48.4:1:34.8:1:0.82054:1.05:60:391:0.3644:0.0167:0.1 0/1:1079:383:173,210:121,152:273,383:0.355:2,2:46.3:1:34.7:1:0.87351:1.03:60:766:0.3569:0.0287:0.2
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chr10 88647906 88647906 T - intronic BMPR1A . . . rs141737683 ID=COSV63135154;OCCURENCE=4(biliary_tract) . . . . . . . . . . . . . . . . 0.1005 0.0717 0.1707 0.1008 0.0423 0.3048 0.0974 0.1371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.2 0.5 279 1009 chr10 88647905 . CT C 279 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1007;VD=246;AF=0.2443;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.27726;SOR=0.93613;LSEQ=GTATGTACACAAACTTCCAG;RSEQ=TTTTTTTTTTTTTTTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1007:246:127,119:347,261:608,246:0.2443:2,2:44.5:1:35:1:0.14949:1.24542:60:492:0.245:0.007:0.1 0/1:1009:259:137,122:340,275:615,259:0.2567:2,2:47:1:34.9:1:0.5519:1.10087:60:518:0.2582:0.0119:0.2
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chr10 88648584 88648584 A - intronic BMPR1A . . . rs11353145 . . . . . . 0.350639 0.6349 . . . . . . . . . 0.2870 0.2503 0.2615 0.3701 0.6445 0.2868 0.2534 0.3042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.2 0.5 306 1456 chr10 88648583 . CA C 306 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1482;VD=450;AF=0.3036;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.11698;SOR=1.1049;LSEQ=AATAGCGTGAGACCATGTCT;RSEQ=AAAAAAAAAAAAAAAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1482:450:306,144:446,203:649,450:0.3036:2,2:40.5:1:34.8:1:0.8431:1.03389:60:449:0.3036:0.0331:1.4 0/1:1456:412:268,144:457,196:653,412:0.283:2,2:40.9:1:34.8:1:0.10525:1.25253:60:411:0.2829:0.0357:1.3
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chr10 88648670 88648672 CTG TTA intronic BMPR1A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.2 0.5 322 1340 chr10 88648670 . CTG TTA 322 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Complex;DP=1464;VD=685;AF=0.4679;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48324;SOR=0.99397;LSEQ=AGCAGCACTTTTTCTGTTAC;RSEQ=TGTGTGCATATGTGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1464:685:321,364:353,386:739,685:0.4679:2,2:42.2:1:34.2:1:0.75009:1.037:60:67.5:0.4701:0.026:2.3 0/1:1340:629:294,335:350,336:686,629:0.4694:2,2:42.1:1:34.6:1:0.12253:1.18677:60:208.667:0.4721:0.0172:2.2
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chr10 89640035 89640035 - T intronic PTEN . . . rs199806546 ID=COSV64288780;OCCURENCE=3(biliary_tract) . . . . . . . . . . . . . . . . 0.0771 0.0612 0.1111 0.1169 0.0153 0.2107 0.0826 0.0892 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.31 0.5 290 927 chr10 89640035 . G GT 290 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=867;VD=297;AF=0.3426;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.36119;SOR=0.96059;LSEQ=AAAGAGTGTACAGTATTTTA;RSEQ=TTTTTTTTTTTTTTTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:867:297:190,106:140,98:238,297:0.3426:2,2:46.7:1:34.9:1:0.21094:1.25:60:594:1:0:0.4 0/1:927:326:203,123:151,87:238,326:0.3517:2,2:46.7:1:34.8:1:0.79191:1.05157:60:325:1:0:0.4
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chr10 89711833 89711833 - T intron PTEN NM_001304718:exon6:UTR5;NM_001304717:exon7:c.1012-42->T;NM_000314:exon6:c.493-42->T . . rs750907391 . . . . . . . . . 2.856e-05 0 0 0 0 0 0 0.0002 3.234e-05 0.0001 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.31 0.25 90 616 chr10 89711833 . A AT 90 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=568;VD=6;AF=0.0106;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.44505;SOR=1.30433;LSEQ=TGAAATAACTATAATGGAAC;RSEQ=TTTTTTTTCAATTTGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:6:6,0:481,56:537,6:0.0106:2,0:30.5:1:35:1:1:0:60:12:0.0112:0.0053:0.2 0/0:616:5:5,0:526,58:584,5:0.0081:2,0:23:1:35:1:1:0:60:10:0.0086:0.0032:0.4
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chr10 89725230 89725230 - T UTR3 PTEN NM_001304718:c.*1_*2insT;NM_001304717:c.*1_*2insT;NM_000314:c.*1_*2insT . . rs756681683 . 539300 Cowden_syndrome_1|Hereditary_cancer-predisposing_syndrome|not_provided MONDO:MONDO:0008021,MedGen:CN072330,OMIM:158350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity . . . 0.0001 0.0002 9.823e-05 0 0 0.0002 0 6.495e-05 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.31 0.5 163 1441 chr10 89725230 . A AT 163 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1469;VD=25;AF=0.017;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.47223;SOR=0.94222;LSEQ=CACAAATTACAAAAGTCTGA;RSEQ=TTTTTTTTTATCAAGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1469:25:9,15:625,744:1369,25:0.017:2,2:49.3:1:34.5:1:0.53645:1.39976:53:50:0.0183:0.0007:0.1 0/1:1441:26:13,12:636,706:1342,26:0.018:2,2:43.2:1:34.8:1:0.68971:1.20:52:52:0.0195:0.0007:0
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chr10 89728634 89728634 T - UTR3 PTEN NM_001304718:c.*3405delT;NM_001304717:c.*3405delT;NM_000314:c.*3405delT . . rs201866164 ID=COSV64293463;OCCURENCE=1(upper_aerodigestive_tract) . . . . . . . . . . . . . . . . 0.0452 0.0137 0.0289 0.0776 0.0125 0.0689 0.0635 0.0633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.31 0.5 294 776 chr10 89728633 . GT G 294 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=806;VD=355;AF=0.4404;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51579;SOR=0.99889;LSEQ=ATGTGAATACAAAGTTTTCA;RSEQ=TTTTTTTTTTCCTGCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:806:355:242,113:283,158:441,355:0.4404:2,2:39.5:1:34.8:1:0.25917:1.20:60:354:0.4403:0.0397:0.2 0/1:776:342:232,110:272,154:426,342:0.4407:2,2:39.9:1:34.9:1:0.25268:1.19:60:341:0.4411:0.0477:0.2
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chr10 96541616 96541616 G A exonic CYP2C19 . synonymous SNV CYP2C19:NM_000769:exon5:c.681G>A:p.P227P rs4244285 ID=COSV64906812;OCCURENCE=4(haematopoietic_and_lymphoid_tissue),7(soft_tissue) . . . . . 0.221446 0.3125 0.1541 0.1892 0.1795 0.1002 0.3104 0.1826 0.1479 0.1672 0.3393 0.1673 0.1792 0.1220 0.1556 0.3125 0.1816 0.1439 0.1728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.33 0.5 340 1738 chr10 96541616 . G A 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1862;VD=882;AF=0.4737;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06542;SOR=0.9021;LSEQ=ACTATCATTGATTATTTCCC;RSEQ=GGAACCCATAACAAATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1862:882:598,284:634,343:977,882:0.4737:2,2:35.9:1:34.8:1:0.20153:1.14:60:440:0.4801:0.0226:1.1 0/1:1738:868:563,305:543,321:864,868:0.4994:2,2:36.2:1:34.9:1:0.39536:1.09:60:1736:0.5061:0.0236:1.1
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chr10 96798548 96798548 C T intronic CYP2C8 . . . rs1934951 ID=COSV64876393;OCCURENCE=2(stomach) . . . . . 0.29972 0.38 . . . . . . . . . 0.2393 0.3448 0.1471 0.2219 0.3800 0.1925 0.1801 0.2251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q23.33 0.5 365 2911 chr10 96798548 . C T 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2832;VD=1412;AF=0.4986;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48573;SOR=1.00329;LSEQ=GTGGTGCTCTTGATCATGGA;RSEQ=AAATAGCAATTCTACCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2832:1412:817,595:844,572:1416,1412:0.4986:2,2:37:1:34.6:1:0.35934:1.07456:60:352:0.5002:0.0244:1.1 0/1:2911:1449:878,571:895,564:1459,1449:0.4978:2,2:37.1:1:34.8:1:0.70385:1.03202:60:723.5:0.5002:0.0323:1.1
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chr10 96827030 96827030 C T exonic CYP2C8 . nonsynonymous SNV CYP2C8:NM_001198854:exon2:c.110G>A:p.R37K,CYP2C8:NM_000770:exon3:c.416G>A:p.R139K,CYP2C8:NM_001198853:exon3:c.206G>A:p.R69K,CYP2C8:NM_001198855:exon4:c.206G>A:p.R69K rs11572080 ID=COSV64875934;OCCURENCE=5(soft_tissue) . . . . . 0.0457268 0.001 0.0853 0.0804 0.0203 0.0650 0.0004 0.1120 0.1134 0.0951 0.0395 0.0744 0.0198 0.0800 0.1026 0 0.1102 0.1040 0.0896 0.188 0.230 T 0.000 0.491 U 0.453 0.327 P 1.61 0.413 L 2.75 0.116 T -1.92 0.461 N -1.014 0.256 T 0.000 0.001 T . . . . . 0.056 0.114 N c -0.477 -0.406 0.000 0.029 0.554 0.246 0 2.8 0.317 0.144 0.158 0.006 0.137 0.008 0.178 0.949 0.424 9.461 0.378 . ENSG00000138115.9 Thyroid 10q23.33 0.5 358 2421 chr10 96827030 . C T 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2504;VD=1247;AF=0.498;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24927;SOR=0.96057;LSEQ=GAACACGGTCCTCAATGCTC;RSEQ=TCTTCCCCATCCCAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2504:1247:631,616:628,622:1250,1247:0.498:2,2:40.1:1:34.9:1:0.87283:1.01:60:414.667:0.4996:0.0156:1.3 1/0:2421:1230:614,616:637,548:1185,1230:0.5081:2,2:39.5:1:34.8:1:0.06106:1.16612:60:409:0.5089:0.0153:1.3
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chr10 104897985 104897985 T C intronic NT5C2 . . . rs11598702 . . . . . . 0.255591 0.2341 . . . . . . . . . 0.2942 0.2030 0.2828 0.3344 0.2217 0.2967 0.3534 0.3051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q24.32 0.5 349 2260 chr10 104897985 . T C 349 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2253;VD=1062;AF=0.4714;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02536;SOR=0.88856;LSEQ=CTAAATTCCTGCATATACCC;RSEQ=AGGTACAGAAAAGAAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2253:1062:620,442:669,517:1186,1062:0.4714:2,2:39.9:1:34.5:1:0.34778:1.08:60:131.75:0.4703:0.0089:1.1 1/0:2260:1132:644,488:620,506:1126,1132:0.5009:2,2:40.1:1:34.5:1:0.39657:1.08:60:101.909:0.4989:0.0159:1.1
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chr10 115439569 115439569 C T exonic CASP7 . nonsynonymous SNV CASP7:NM_001267057:exon1:c.56C>T:p.T19I rs7921977 ID=COSV61880912;OCCURENCE=1(large_intestine),23(upper_aerodigestive_tract) . . . . . 0.854233 0.8224 . 0.8663 0.8973 0.8065 0.7719 . 0.8688 0.8171 0.8683 0.8485 0.9632 0.6466 0.8775 0.8027 0.8059 0.8100 0.8037 . . . . . . 1.000 0.198 P . . . . . . . . . . . . . . . . . . . . 0.000 0.001 N n 0.848 4.527 1.000 0.747 0.031 0.002 2 -0.152 0.127 -2.054 0.015 -1.105 0.018 0.000 0.063 0.000 0.016 7.439 0.262 . . . 10q25.3 0.5 363 2745 chr10 115439569 . C T 363 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2864;VD=1475;AF=0.515;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04351;SOR=1.09729;LSEQ=CACCCCTGCGGAGCGCACTA;RSEQ=CCCGAGCCAGGGGCGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2864:1475:792,683:714,672:1386,1475:0.515:2,2:38.3:1:34.5:1:0.24575:1.09:60:121.917:0.5146:0.014:1.1 0/1:2745:1350:759,591:742,648:1390,1350:0.4918:2,2:39:1:34.5:1:0.14462:1.12:60:102.846:0.4924:0.0044:1.2
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chr10 115439641 115439642 TT - exonic CASP7 . frameshift deletion CASP7:NM_001267057:exon1:c.128_129del:p.L44Sfs*70 rs10553596 ID=COSV61881099;OCCURENCE=1(stomach),10(upper_aerodigestive_tract) . . . . . 0.290735 0.252 . 0.2927 0.3925 0.2273 0.2266 0.5 0.3379 0.2288 0.2771 0.2673 0.3881 0.1930 0.3667 0.2320 0.1970 0.2229 0.2147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q25.3 0.5 353 2095 chr10 115439640 . CTT C 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2215;VD=1130;AF=0.5102;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.20052;SOR=1.05444;LSEQ=CTCCCTCCGCAGCGCCGAGA;RSEQ=TTAGTTTCGCTTTCGCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2215:1130:451,679:463,622:1085,1130:0.5102:2,2:42.2:1:34.9:1:0.19537:1.12063:60:1129:0.5109:0.0293:0.8 0/1:2095:1041:425,616:430,623:1053,1041:0.4969:2,2:42.4:1:34.8:1:1:1.0004:60:1040:0.4974:0.0353:0.8
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chr10 115489152 115489152 C G exonic CASP7 . nonsynonymous SNV CASP7:NM_001267058:exon6:c.690C>G:p.D230E,CASP7:NM_001227:exon7:c.765C>G:p.D255E,CASP7:NM_001267056:exon7:c.765C>G:p.D255E,CASP7:NM_001267057:exon7:c.1020C>G:p.D340E,CASP7:NM_001320911:exon7:c.789C>G:p.D263E,CASP7:NM_033338:exon8:c.864C>G:p.D288E,CASP7:NM_033339:exon8:c.765C>G:p.D255E,CASP7:NM_033340:exon8:c.731C>G:p.T244S rs2227310 ID=COSV61881355;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) 1236524 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.2498 0.4157 0.2161 0.2607 0.1385 0.2855 0.4221 0.2774 0.2574 0.2536 0.2387 0.2425 0.1415 0.2697 0.1755 0.4245 0.2708 0.2722 0.2832 0.842 0.028 T 0.514 0.118 N 1.000 0.199 P . . . 1.9 0.235 T 0.96 0.015 N -0.917 0.459 T 0.000 0.000 T . . . . . 0.087 0.144 N c -0.775 -0.701 0.004 0.102 0.706 0.609 0 1.66 0.230 -0.741 0.049 0.935 0.490 0.005 0.169 0.984 0.507 6.114 0.192 Caspase-like domain|Peptidase C14, caspase non-catalytic subunit p10|Peptidase C14A, caspase catalytic domain ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000197893.9|ENSG00000148735.10|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15 Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Coronary|Artery_Tibial|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Nerve_Tibial|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Spleen|Stomach|Testis|Testis|Thyroid|Vagina|Whole_Blood 10q25.3 0.5 334 1660 chr10 115489152 . C G 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1748;VD=847;AF=0.4846;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42103;SOR=0.98411;LSEQ=CTGGAGGAGCACGGAAAAGA;RSEQ=CTGGAAATCATGCAGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1748:847:457,390:498,402:900,847:0.4846:2,2:39.1:1:34.4:1:0.56439:1.05713:60:93.111:0.4855:0.0143:2 0/1:1660:811:437,374:482,363:845,811:0.4886:2,2:39.6:1:34.5:1:0.19888:1.13631:60:114.857:0.4896:0.0151:2
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chr10 115489167 115489167 G A exonic CASP7 . nonsynonymous SNV CASP7:NM_033340:exon8:c.746G>A:p.R249K rs2227309 ID=COSV61881361;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) . . . . . 0.2498 0.4087 0.2172 0.2604 0.1420 0.2855 0.4160 0.2774 0.2572 0.2536 0.2385 0.2429 0.1453 0.2703 0.1722 0.4212 0.2706 0.2713 0.2831 1.0 0.010 T . . . 0.964 0.810 P . . . 3.07 0.086 T 0.06 0.063 N -0.927 0.447 T 0.000 0.000 T . . . . . 0.960 0.670 D c 0.055 0.191 0.674 0.224 0.706 0.609 0 3.97 0.451 4.101 0.573 0.097 0.197 1.000 0.715 1.000 0.888 11.314 0.484 Caspase-like domain|Peptidase C14, caspase non-catalytic subunit p10|Peptidase C14A, caspase catalytic domain ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15|ENSG00000197893.9|ENSG00000148735.10|ENSG00000165806.15|ENSG00000165806.15|ENSG00000165806.15 Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Coronary|Artery_Tibial|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Nerve_Tibial|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Spleen|Stomach|Testis|Testis|Thyroid|Vagina|Whole_Blood 10q25.3 0.5 332 1537 chr10 115489167 . G A 332 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1587;VD=748;AF=0.4713;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24942;SOR=0.9503;LSEQ=AAAGACCTGGAAATCATGCA;RSEQ=ATCCTCACCAGGGTGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1587:748:394,354:458,373:831,748:0.4713:2,2:42.9:1:34.8:1:0.33712:1.10315:60:248.333:0.473:0.0063:2.1 0/1:1537:744:379,365:450,342:792,744:0.4841:2,2:42.3:1:34.8:1:0.02129:1.26698:60:371:0.485:0.0124:2.1
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chr10 115489589 115489589 T C UTR3 CASP7 NM_001267056:c.*290T>C;NM_001320911:c.*290T>C;NM_033340:c.*406T>C;NM_001267057:c.*290T>C;NM_033338:c.*290T>C;NM_033339:c.*290T>C;NM_001227:c.*290T>C;NM_001267058:c.*290T>C . . rs4353229 . . . . . . 0.251797 0.4157 . . . . . . . . . 0.2433 0.1450 0.2697 0.1755 0.4257 0.2715 0.2715 0.2827 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q25.3 0.5 352 2413 chr10 115489589 . T C 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2461;VD=1207;AF=0.4905;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19684;SOR=1.0518;LSEQ=ATACATGCAACAGAAGTGAC;RSEQ=TCTGGAGAAAGCTCATGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2461:1207:751,456:768,484:1252,1207:0.4905:2,2:37.8:1:34.4:1:0.67812:1.04:60:91.846:0.4877:0.0142:1.1 0/1:2413:1153:694,459:805,453:1258,1153:0.4778:2,2:37.8:1:34.5:1:0.05854:1.17522:60:103.818:0.4764:0.0091:1.1
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chr10 123239112 123239112 G A exonic FGFR2 . synonymous SNV FGFR2:NM_001144915:exon17:c.2107C>T:p.L703L rs1047057 ID=COSV60638447;OCCURENCE=14(meninges),1(haematopoietic_and_lymphoid_tissue),1(stomach),17(soft_tissue),1(upper_aerodigestive_tract) 309584 Craniosynostosis_syndrome|Crouzon_syndrome|Saethre-Chotzen_syndrome|Beare-Stevenson_cutis_gyrata_syndrome|Isolated_coronal_synostosis|not_specified|not_provided Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|Human_Phenotype_Ontology:HP:0004439,MONDO:MONDO:0007405,MeSH:D003394,MedGen:C0010273,OMIM:123500,Orphanet:ORPHA207,SNOMED_CT:28861008|MONDO:MONDO:0007042,MedGen:C0175699,OMIM:101400,Orphanet:ORPHA794,SNOMED_CT:83015004|MONDO:MONDO:0007412,MedGen:C1852406,OMIM:123790,Orphanet:ORPHA1555|MedGen:CN043619|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.414337 0.3512 0.4345 0.5410 0.1494 0.6937 0.3624 0.6136 0.5638 0.6111 0.6055 0.4191 0.1433 0.7254 0.5567 0.3736 0.4908 0.5431 0.4929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q26.13 1 381 2054 chr10 123239112 . G A 381 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2035;VD=2026;AF=0.9956;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20817;SOR=1.54471;LSEQ=GTCCTACTGGTCCACAGCCA;RSEQ=TACGCACGGCAGGTGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2035:2026:1355,671:0,0:0,2026:0.9956:0,2:39.8:1:34.8:1:1:0:60:252.25:0.9975:0.0162:1.1 1/1:2054:2040:1363,677:1,0:1,2040:0.9932:0,2:39.3:1:34.7:1:1:0:60:254:0.9956:0.019:1.1
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chr10 123298158 123298158 T C exonic FGFR2 . synonymous SNV FGFR2:NM_001144916:exon3:c.351A>G:p.V117V,FGFR2:NM_001144918:exon4:c.351A>G:p.V117V,FGFR2:NM_023029:exon4:c.429A>G:p.V143V,FGFR2:NM_001144913:exon5:c.696A>G:p.V232V,FGFR2:NM_001144914:exon5:c.696A>G:p.V232V,FGFR2:NM_001144915:exon5:c.429A>G:p.V143V,FGFR2:NM_001144919:exon5:c.429A>G:p.V143V,FGFR2:NM_000141:exon6:c.696A>G:p.V232V,FGFR2:NM_001144917:exon6:c.696A>G:p.V232V,FGFR2:NM_001320658:exon6:c.696A>G:p.V232V,FGFR2:NM_022970:exon6:c.696A>G:p.V232V rs1047100 ID=COSV100335254;OCCURENCE=17(meninges),2(central_nervous_system) 253704 Craniosynostosis_syndrome|Crouzon_syndrome|Saethre-Chotzen_syndrome|Beare-Stevenson_cutis_gyrata_syndrome|Isolated_coronal_synostosis|not_specified|FGFR2_related_craniosynostosis Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|Human_Phenotype_Ontology:HP:0004439,MONDO:MONDO:0007405,MeSH:D003394,MedGen:C0010273,OMIM:123500,Orphanet:ORPHA207,SNOMED_CT:28861008|MONDO:MONDO:0007042,MedGen:C0175699,OMIM:101400,Orphanet:ORPHA794,SNOMED_CT:83015004|MONDO:MONDO:0007412,MedGen:C1852406,OMIM:123790,Orphanet:ORPHA1555|MedGen:CN043619|MedGen:CN169374|MedGen:CN231480 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.795327 0.9355 0.7667 0.7800 0.7474 0.8181 0.9232 0.7464 0.7715 0.7997 0.7441 0.7635 0.7530 0.8126 0.8676 0.9030 0.7590 0.7519 0.7459 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10q26.13 1 398 2776 chr10 123298158 . T C 398 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2927;VD=2914;AF=0.9956;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22638;SOR=0.64789;LSEQ=GACCCGTATTCATTCTCCAC;RSEQ=ACACAGGTATAATTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2927:2914:1583,1331:2,2:4,2914:0.9956:2,2:38.5:1:34.6:1:1:1.19:60:131.455:0.9976:0.0355:1.1 1/1:2776:2768:1513,1255:0,0:0,2768:0.9971:0,2:39:1:34.6:1:1:0:60:172:0.9993:0.0169:1.1
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chr11 4104007 4104007 C A intronic STIM1 . . . rs16929438 . 1219643 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.086262 0.1845 . . . . . . . . . 0.0579 0.0792 0.1563 0.0397 0.1981 0.0552 0.0277 0.0305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 374 2865 chr11 4104007 . C A 374 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3025;VD=1724;AF=0.5699;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18413;SOR=0.9523;LSEQ=TCCCTTTCCTTGTACAGCCT;RSEQ=AGTTGTGCTAGGAGGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3025:1724:958,766:709,589:1298,1724:0.5699:2,2:41.2:1:34.8:1:0.60523:1.04:60:861:0.5729:0.0129:1.9 1/0:2865:1667:900,767:617,578:1195,1667:0.5818:2,2:41.5:1:34.6:1:0.22432:1.10:60:184.222:0.582:0.0119:1.9
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chr11 4104060 4104060 A C intronic STIM1 . . . rs2898950 . 1282054 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.8125 0.9603 0.7995 . . . . . . . . 0.8104 0.5509 0.9344 0.8543 0.9524 0.9112 0.9102 0.8709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 1 399 3208 chr11 4104060 . A C 399 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3279;VD=3273;AF=0.9982;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28852;SOR=1.53459;LSEQ=GGGGAAGGCCTTTCTCATTT;RSEQ=TTCCATTCTCGAATCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3279:3273:1655,1618:0,0:0,3273:0.9982:0,2:36.8:1:34.2:1:1:0:60:75.116:0.9985:0.0366:1.8 1/1:3208:3199:1554,1645:0,0:0,3199:0.9972:0,2:37.1:1:34.5:1:1:0:60:198.938:0.9975:0.0371:1.8
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chr11 4104087 4104087 T C intron STIM1 NM_001277962:exon9:c.1138-25T>C;NM_003156:exon9:c.1138-25T>C;NM_001277961:exon9:c.1138-25T>C . . rs10767828 . 1217683 Stormorken_syndrome|Combined_immunodeficiency_due_to_STIM1_deficiency|Myopathy,_tubular_aggregate,_1|not_provided MONDO:MONDO:0008497,MedGen:C1861451,OMIM:185070,Orphanet:ORPHA3204|MONDO:MONDO:0013008,MedGen:C2748557,OMIM:612783,Orphanet:ORPHA317430|MONDO:MONDO:0024531,MedGen:C4011726,OMIM:160565|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.663738 0.7758 0.6764 0.8072 0.2646 0.7729 0.7586 0.8511 0.8739 0.8415 0.9117 0.6924 0.2698 0.7572 0.8046 0.7559 0.8549 0.8786 0.8221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 351 3096 chr11 4104087 . T C 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3101;VD=1212;AF=0.3908;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42712;SOR=1.01099;LSEQ=TCTCGAATCCCTGCTCTTTT;RSEQ=GAGCTGGGGGCCTCATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3101:1212:617,595:946,943:1889,1212:0.3908:2,2:36.8:1:34.3:1:0.65888:1.03:60:85.571:0.3882:0.009:1.9 0/1:3096:1202:596,606:938,954:1892,1202:0.3882:2,2:36.8:1:34.5:1:1:1.00:60:239.4:0.3876:0.0207:1.9
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chr11 4113395 4113395 G A UTR3 STIM1 NM_001277962:c.*839G>A;NM_003156:c.*367G>A;NM_001277961:c.*367G>A . . rs1561876 . . . . . . 0.694089 0.7669 . . . . . . . . . 0.7261 0.3823 0.7667 0.8079 0.7466 0.8568 0.8822 0.8323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 352 3088 chr11 4113395 . G A 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3066;VD=1122;AF=0.3659;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.147;SOR=0.94488;LSEQ=TGTTTCTGTCTCTTGCTTTC;RSEQ=GGCTCCTCCCTCCCACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3066:1122:675,447:1166,767:1933,1122:0.3659:2,2:37.8:1:34.7:1:0.93889:1.00671:60:560:0.3681:0.0147:1.1 0/1:3088:1171:722,449:1152,761:1913,1171:0.3792:2,2:37:1:34.6:1:0.44733:1.06:60:194.167:0.3805:0.0149:1.1
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chr11 4113470 4113470 T G UTR3 STIM1 NM_001277962:c.*914T>G;NM_003156:c.*442T>G;NM_001277961:c.*442T>G . . rs3750994 . . . . . . 0.0678914 0.1925 . . . . . . . . . 0.0362 0.0095 0.1492 0.0364 0.1999 0.0538 0.0245 0.0234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 362 2593 chr11 4113470 . T G 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2512;VD=1504;AF=0.5987;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.21111;SOR=0.95351;LSEQ=GACGAGTAGCTTCTGACATG;RSEQ=GTGCCTCAGATCTGTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2512:1504:732,772:487,515:1002,1504:0.5987:2,2:43.8:1:34.5:1:1:1.00:60:106.429:0.5984:0.0036:1.1 1/0:2593:1582:766,816:484,523:1007,1582:0.6101:2,2:42.1:1:34.1:1:0.87186:1.01:60:59.846:0.6069:0.0181:1.1
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chr11 4115541 4115541 G A upstream RRM1 dist=374 . . rs16929410 . . . . . . 0.0640974 0.1845 . . . . . . . . . 0.0294 0.0068 0.1348 0.0232 0.1947 0.0524 0.0142 0.0193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 374 2889 chr11 4115541 . G A 374 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2927;VD=1773;AF=0.6057;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46784;SOR=1.00578;LSEQ=CCAAACGCCATCGGCCTTGC;RSEQ=CGGTTTTCTTCCAGTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2927:1773:801,972:568,571:1139,1773:0.6057:2,2:41.6:1:34.7:1:0.01345:1.20702:60:353.6:0.6099:0.0188:1.1 1/0:2889:1746:764,982:483,644:1127,1746:0.6044:2,2:41:1:34.6:1:0.6438:1.04:60:157.727:0.6069:0.0246:1.1
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chr11 4115560 4115561 AG - upstream RRM1 dist=354 . . rs398054921 . . . . . . 0.0638978 0.1845 . . . . . . . . . 0.0294 0.0068 0.1348 0.0233 0.1957 0.0524 0.0142 0.0194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 368 2474 chr11 4115559 . CAG C 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2548;VD=1509;AF=0.5922;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.28829;SOR=1.03425;LSEQ=GCGCGGTTTTCTTCCAGTTC;RSEQ=AGTGTCAGTCCTCTGGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2548:1509:634,875:479,552:1031,1509:0.5922:2,2:42:1:34.9:1:0.02791:1.19752:60:3018:0.5932:0.0463:1.1 1/0:2474:1445:586,859:403,623:1026,1445:0.5841:2,2:43:1:35:1:0.53221:1.05:60:2890:0.5845:0.042:1.1
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chr11 4159457 4159457 A G exonic RRM1 . synonymous SNV RRM1:NM_001318065:exon13:c.1209A>G:p.T403T,RRM1:NM_001330193:exon13:c.1557A>G:p.T519T,RRM1:NM_001318064:exon18:c.1932A>G:p.T644T,RRM1:NM_001033:exon19:c.2223A>G:p.T741T rs9937 ID=COSV56163380;OCCURENCE=1(stomach),3(haematopoietic_and_lymphoid_tissue),2(thyroid) . . . . . 0.344649 0.3819 0.4112 0.4573 0.1503 0.4660 0.3847 0.4596 0.5344 0.4632 0.3945 0.3995 0.1575 0.4438 0.4867 0.3716 0.4790 0.5181 0.4395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 324 1922 chr11 4159457 . A G 324 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1995;VD=708;AF=0.3549;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26826;SOR=1.04465;LSEQ=GGGATGTATTATTTAAGGAC;RSEQ=AGACCAGCGGCTAATCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1995:708:394,314:671,615:1286,708:0.3549:2,2:42.2:1:34.3:1:0.14593:1.15:60:117:0.3531:0.011:2.1 0/1:1922:663:381,282:666,591:1257,663:0.345:2,2:41.5:1:34.4:1:0.06699:1.20:60:164.75:0.3439:0.0151:2.1
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chr11 4159466 4159466 G A exonic RRM1 . synonymous SNV RRM1:NM_001318065:exon13:c.1218G>A:p.A406A,RRM1:NM_001330193:exon13:c.1566G>A:p.A522A,RRM1:NM_001318064:exon18:c.1941G>A:p.A647A,RRM1:NM_001033:exon19:c.2232G>A:p.A744A rs1042858 ID=COSV56164351;OCCURENCE=1(stomach),1(haematopoietic_and_lymphoid_tissue),1(thyroid) . . . . . 0.845647 0.7619 0.8933 0.8909 0.8138 0.8079 0.7425 0.8896 0.9267 0.9072 0.9426 0.8784 0.8104 0.8141 0.91 0.7435 0.8956 0.9311 0.8832 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11p15.4 0.5 327 1816 chr11 4159466 . G A 327 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1912;VD=670;AF=0.3504;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31825;SOR=1.03555;LSEQ=TATTTAAGGACAAGACCAGC;RSEQ=GCTAATCCAATCCAGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1912:670:353,317:640,595:1235,670:0.3504:2,2:42.5:1:34.9:1:0.73682:1.04:60:669:0.354:0.0146:2.1 0/1:1816:622:345,277:606,583:1189,622:0.3425:2,2:43.9:1:34.8:1:0.07445:1.20:60:310:0.3446:0.0044:2.1
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chr11 67352689 67352689 A G exonic GSTP1 . nonsynonymous SNV GSTP1:NM_000852:exon5:c.313A>G:p.I105V rs1695 ID=COSV66992376;OCCURENCE=1(breast),1(large_intestine),7(soft_tissue),1(lung) 37785 Neoplasm_of_the_large_intestine|not_provided Human_Phenotype_Ontology:HP:0100834,MeSH:D015179,MedGen:C0009404,SNOMED_CT:126837005|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.352636 0.1786 0.3608 0.3325 0.4459 0.5374 0.1753 0.2749 0.3159 0.2868 0.2888 0.3537 0.4496 0.4737 0.25 0.1718 0.2695 0.3351 0.3172 1.0 0.010 T 0.320 0.041 N . . . -0.095 0.047 N 3.96 0.034 T 0.29 0.043 N -0.938 0.429 T 0.000 0.000 T . . . . . 0.009 0.034 N c -2.101 -2.017 1.000 0.747 0.628 0.401 0 -1.16 0.091 -1.459 0.025 -0.811 0.031 0.000 0.063 0.009 0.108 6.983 0.237 Glutathione S-transferase, C-terminal-like;Glutathione S-transferase, C-terminal|Glutathione S-transferase, C-terminal-like ENSG00000213402.2|ENSG00000084207.11|ENSG00000167792.7|ENSG00000084207.11|ENSG00000213402.2|ENSG00000084207.11|ENSG00000231793.4|ENSG00000255318.1|ENSG00000167799.5|ENSG00000084207.11|ENSG00000213402.2|ENSG00000084207.11|ENSG00000213402.2|ENSG00000084207.11|ENSG00000231793.4|ENSG00000084207.11|ENSG00000084207.11|ENSG00000084207.11|ENSG00000084207.11|ENSG00000084207.11|ENSG00000167799.5|ENSG00000213402.2|ENSG00000084207.11|ENSG00000175634.10|ENSG00000213402.2|ENSG00000231793.4|ENSG00000213402.2|ENSG00000084207.11|ENSG00000231793.4|ENSG00000213402.2|ENSG00000255318.1|ENSG00000175634.10|ENSG00000213402.2|ENSG00000231793.4|ENSG00000213402.2|ENSG00000084207.11|ENSG00000231793.4|ENSG00000255318.1|ENSG00000175634.10|ENSG00000167799.5|ENSG00000175634.10|ENSG00000213402.2|ENSG00000084207.11|ENSG00000167799.5|ENSG00000167799.5|ENSG00000167792.7|ENSG00000175634.10|ENSG00000213402.2|ENSG00000110711.5|ENSG00000084207.11|ENSG00000255119.1|ENSG00000213402.2|ENSG00000167792.7|ENSG00000213402.2|ENSG00000213402.2|ENSG00000167792.7|ENSG00000231793.4|ENSG00000175634.10|ENSG00000213402.2|ENSG00000167792.7|ENSG00000231793.4|ENSG00000175634.10|ENSG00000213402.2|ENSG00000110711.5|ENSG00000084207.11|ENSG00000213402.2|ENSG00000167792.7|ENSG00000255318.1|ENSG00000231793.4 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Artery_Aorta|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hypothalamus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Nucleus_accumbens_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Heart_Left_Ventricle|Heart_Left_Ventricle|Heart_Left_Ventricle|Liver|Lung|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Testis|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Whole_Blood 11q13.2 0.5 354 2486 chr11 67352689 . A G 354 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2504;VD=1235;AF=0.4932;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22248;SOR=0.95611;LSEQ=AGGACCTCCGCTGCAAATAC;RSEQ=TCTCCCTCATCTACACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2504:1235:671,564:705,561:1266,1235:0.4932:2,2:40:1:34.5:1:0.52012:1.05624:60:111.273:0.4918:0.0176:1.1 1/0:2486:1254:713,541:689,541:1230,1254:0.5044:2,2:40.3:1:34.4:1:0.6858:1.03:60:113:0.5028:0.0177:1.1
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chr11 67353579 67353579 C T exonic GSTP1 . nonsynonymous SNV GSTP1:NM_000852:exon6:c.341C>T:p.A114V rs1138272 ID=COSV66992270;OCCURENCE=3(soft_tissue),2(lung) 37787 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0335463 0.001 0.0601 0.0602 0.0147 0.0253 0.0001 0.0834 0.0773 0.0859 0.0695 0.0605 0.0156 0.0263 0.0397 0.0006 0.0832 0.0891 0.0779 0.251 0.170 T 0.949 0.083 N . . . 2.105 0.586 M 3.7 0.041 T -1.88 0.439 N -0.991 0.323 T 0.001 0.003 T . . . . . 0.191 0.203 N c -0.579 -0.690 1.000 0.747 0.722 0.854 0 0.531 0.162 0.032 0.135 0.020 0.144 0.031 0.203 0.502 0.271 6.256 0.200 Glutathione S-transferase, C-terminal-like;Glutathione S-transferase, C-terminal|Glutathione S-transferase, C-terminal-like ENSG00000213402.2|ENSG00000231793.4|ENSG00000175634.10|ENSG00000255119.1|ENSG00000175505.9|ENSG00000167792.7|ENSG00000175634.10 Adipose_Subcutaneous|Brain_Cerebellum|Esophagus_Mucosa|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg 11q13.2 0.5 362 2961 chr11 67353579 . C T 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3131;VD=1592;AF=0.5085;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23363;SOR=1.03936;LSEQ=TGGTGGTGTCTGGCAGGAGG;RSEQ=GGGCAAGGATGACTATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3131:1592:1056,536:979,554:1533,1592:0.5085:2,2:38.3:1:34.1:1:0.15374:1.11:60:74.81:0.5111:0.0192:1.1 0/1:2961:1477:1000,477:991,483:1474,1477:0.4988:2,2:39.7:1:34.1:1:0.81363:1.02:60:55.808:0.5014:0.0071:1.1
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chr11 69462910 69462910 G A exonic CCND1 . synonymous SNV CCND1:NM_053056:exon4:c.723G>A:p.P241P rs9344 ID=COSV57118864;OCCURENCE=1(salivary_gland),12(meninges),2(central_nervous_system),2(haematopoietic_and_lymphoid_tissue),1(urinary_tract),18(soft_tissue),1(prostate),1(thyroid) 28794 VON_HIPPEL-LINDAU_SYNDROME,_MODIFIER_OF|Colorectal_cancer,_susceptibility_to|Multiple_myeloma,_translocation_11,14_type|not_provided .|MedGen:C1858438|MedGen:CN186214|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.413538 0.5714 0.3867 0.4556 0.2138 0.3758 0.5680 0.4830 0.4715 0.4971 0.5240 0.3966 0.2158 0.4125 0.4801 0.5495 0.4808 0.4583 0.4713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q13.3 0.5 365 2839 chr11 69462910 . G A 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2891;VD=1429;AF=0.4943;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30334;SOR=1.02903;LSEQ=AGAGTGATCAAGTGTGACCC;RSEQ=GTAAGTGAGGGTGATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2891:1429:705,724:695,760:1455,1429:0.4943:2,2:39.3:1:34.9:1:0.41244:1.06:60:713.5:0.4951:0.008:1.1 0/1:2839:1383:662,721:714,740:1454,1383:0.4871:2,2:40:1:35:1:0.523:1.05081:60:2766:0.4903:0.0053:1.1
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chr11 69465873 69465874 CT - splicing CCND1 NM_053056:exon5:r.spl . . rs766706465 . . . . . . . . . 0.0003 0.0001 0.0001 0.0003 0 0.0003 0 0.0003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q13.3 0.5 175 2619 chr11 69465872 . CCT C 175 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2667;VD=32;AF=0.012;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.37422;SOR=0.89661;LSEQ=CTCTTCCCACCTCTCCCCAC;RSEQ=CTCTCTCTCAGGACTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2667:32:18,14:1619,1011:2630,32:0.012:2,2:38:1:35:1:0.58521:1.2454:60:64:0.0121:0.0019:0.3 0/1:2619:35:26,9:1652,931:2583,35:0.0134:2,2:34.9:1:34.3:1:0.28669:1.63:60:70:0.0134:0.0019:0.1
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chr11 69465988 69465990 GAG - exonic CCND1 . nonframeshift deletion CCND1:NM_053056:exon5:c.826_828del:p.E280del rs753296543 ID=COSV57120755;OCCURENCE=2(large_intestine),1(endometrium) . . . . . . . . 0.0012 0.0004 0.0020 0.0016 0.0002 0.0010 0.0018 0.0023 6.478e-05 0 0.0012 0 0 0 6.689e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q13.3 0.25 176 2892 chr11 69465987 . AGAG A 176 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=2811;VD=26;AF=0.0092;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.21263;SOR=0.78479;LSEQ=AAGGCCGCCGAGGAGGAGGA;RSEQ=GAGGAGGAGGAGGTGGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2811:26:17,9:1556,1225:2781,26:0.0092:2,2:44.8:1:34.6:1:0.42826:1.49:60:52:0.0093:0:0.5 0/1:2892:34:20,14:1597,1259:2856,34:0.0118:2,2:43:1:34.7:1:0.86243:1.13:60:68:0.0118:0.0014:0.4
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chr11 94198548 94198549 TC - intronic MRE11 . . . . . . . . . . . . . . . . . . . . . 0.0010 0.0027 0 0.0034 0 0 0.0002 0.0024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q21 0.25 136 816 chr11 94198547 . ATC A 136 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=856;VD=5;AF=0.0058;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.01543;SOR=0.31394;LSEQ=ATTTTTGTATTACCCAGACC;RSEQ=TCTCTCTCTCTCTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:856:5:1,4:385,465:850,5:0.0058:2,2:17.4:1:35:1:0.38531:3.30776:60:10:0.0059:0.0035:0.8 0/1:816:15:5,10:359,440:799,15:0.0184:2,2:39.5:1:35:1:0.43967:1.63087:60:30:0.0187:0.0086:0.7
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chr11 103418158 103418158 A G intergenic DYNC2H1;MIR4693 dist=67567;dist=302476 . . rs716274 . . . . . . 0.437101 0.2877 . . . . . . . . . 0.5041 0.4492 0.3699 0.55 0.2481 0.5624 0.5553 0.5265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 1 350 1125 chr11 103418158 . A G 350 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1122;VD=1119;AF=0.9973;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31133;SOR=0.33198;LSEQ=GGGGCCAGTGACAAGCCTCA;RSEQ=CTAAGGCTCAGGTATGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1122:1119:630,489:1,0:1,1119:0.9973:0,2:40:1:34.3:1:1:0:60:78.929:0.9991:0.0285:2 1/1:1125:1124:623,501:0,0:0,1124:0.9991:0,2:40.5:1:34.6:1:1:0:60:186.333:0.9991:0.0213:2
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chr11 103418177 103418177 T C intergenic DYNC2H1;MIR4693 dist=67586;dist=302457 . . rs10895459 . . . . . . 0.261581 0.1855 . . . . . . . . . 0.3345 0.1666 0.2434 0.4801 0.1480 0.4330 0.4278 0.3918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 304 988 chr11 103418177 . T C 304 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=972;VD=429;AF=0.4414;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.44744;SOR=0.98398;LSEQ=AACTAAGGCTCAGGTATGAT;RSEQ=AGAGAGCTGCTAATAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:972:429:225,204:280,263:543,429:0.4414:2,2:41.2:1:34.5:1:0.79623:1.04:60:213.5:0.442:0.0123:2.5 0/1:988:440:227,213:286,262:548,440:0.4453:2,2:42:1:34.7:1:0.89806:1.02426:60:439:0.4452:0.0132:2.4
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chr11 108107261 108107261 - A intronic ATM . . . rs11418587 . . . . . . 0.316094 0.2698 . . . . . . . . . 0.5002 0.3888 0.5825 0.5935 0.4159 0.5468 0.5616 0.5928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 289 1040 chr11 108107261 . T TA 289 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1062;VD=324;AF=0.3051;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.0309;SOR=1.20326;LSEQ=AGTGAGACCCTGTTTCCATT;RSEQ=AAAAAAAAAAAAAAAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1062:324:196,127:284,160:444,324:0.3051:2,2:46.1:1:34.7:1:0.36521:1.14991:60:323:0.746:0:0.1 0/1:1040:278:171,106:291,171:462,278:0.2673:2,2:47.4:1:34.7:1:0.75385:1.0548:60:277:0.5996:0:0.2
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chr11 108119616 108119616 A - intron ATM NM_000051:exon9:c.1066-44A>-;NM_001351834:exon10:c.1066-44A>- . . rs35813860 . 1222845 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.3571 0.3244 0.3434 0.3599 0.3443 0.3570 0.3232 0.3717 0.0153 0.0047 0.0614 0.0385 0 0.1936 0.0115 0.0267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 271 1112 chr11 108119615 . CA C 271 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1089;VD=222;AF=0.2039;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.32342;SOR=1.05609;LSEQ=ACAACAGCGAAACTCTGGCT;RSEQ=AAAAAAAAAAAAAGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1089:222:168,54:560,182:742,222:0.2039:2,2:39.7:1:34.8:1:1:1.01:60:110:0.2024:0.0202:0.1 0/1:1112:217:158,59:558,196:754,217:0.1951:2,2:38.1:1:34.9:1:0.7268:1.06303:60:434:0.1955:0.027:0.2
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chr11 108121410 108121410 - T intron ATM NM_000051:exon10:c.1236-18->T;NM_001351834:exon11:c.1236-18->T . . rs34325032 ID=COSV53729214;OCCURENCE=29(ovary),1(central_nervous_system) 180398 Hereditary_cancer-predisposing_syndrome|not_specified|Breast_and/or_ovarian_cancer|not_provided MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN221562|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.40595 0.3641 0.3252 0.3705 0.3188 0.3899 0.3064 0.4225 0.3741 0.3876 0.3769 0.5019 0.4265 0.5668 0.5875 0.4125 0.4710 0.5539 0.5839 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 314 1955 chr11 108121410 . C CT 314 PASS STATUS=AFDiff;SAMPLE=NCCL202312;TYPE=Insertion;DP=1967;VD=511;AF=0.2598;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.05186;SOR=1.13092;LSEQ=GGAATAGTTTTCAAATTATC;RSEQ=TTTTTTTTTTTTTTTAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1967:511:331,180:523,239:762,511:0.2598:2,2:42.5:1:35:1:0.16177:1.18983:60:1022:0.7137:0:0.1 0/1:1955:463:303,159:596,281:877,463:0.2368:2,2:43:1:34.9:1:0.39187:1.11291:60:462:0.5448:0:0.1
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chr11 108126150 108126151 TT - intronic ATM . . . rs538304080 . . . . . . 0.740815 0.8095 . . . . . . . . . 0.4420 0.4952 0.3664 0.3816 0.5317 0.2595 0.4170 0.3526 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 272 853 chr11 108126149 . CTT C 272 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=846;VD=212;AF=0.2506;SHIFT3=19;MSI=21.000;MSILEN=1;SSF=0.24965;SOR=0.92218;LSEQ=ATTCTATAAAATTGTCTAAA;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:846:212:88,124:142,99:241,212:0.2506:2,2:46.6:1:34.8:1:0.00024:2.01793:60:424:0.2515:0.0201:0.2 0/1:853:227:98,129:103,108:211,227:0.2661:2,2:45.8:1:34.8:1:0.25047:1.25472:60:226:0.2659:0.0234:0.2
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chr11 108151698 108151698 T - intron ATM NM_000051:exon24:c.3403-24T>-;NM_001351834:exon25:c.3403-24T>- . . rs781372237 ID=COSV53726508;OCCURENCE=1(large_intestine),18(ovary) . . . . . . . 0.0035 0.0022 0.0008 0.0021 0.0020 0.0005 0.0024 0.0023 0.0032 0.0004 0.0003 0 0 0.0014 0.0005 0.0003 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 210 1722 chr11 108151697 . AT A 210 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1741;VD=64;AF=0.0368;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1002;SOR=1.3029;LSEQ=ACATTTACATTTTACATTAC;RSEQ=TTTTTTTTTAATTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1741:64:45,19:1173,504:1677,64:0.0368:2,2:41.2:1:35:1:1:1.02:60:128:0.0369:0.0023:0.2 0/1:1722:49:34,15:1157,515:1672,49:0.0285:2,2:42.7:1:35:1:1:1.01:60:98:0.0285:0.0012:0.1
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chr11 108151707 108151707 - A intron ATM NM_000051:exon24:c.3403-15->A;NM_001351834:exon25:c.3403-15->A . . rs3218681 ID=COSV53729230;OCCURENCE=29(ovary),2(central_nervous_system) 180443 Ataxia-telangiectasia_syndrome|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|Breast_and/or_ovarian_cancer|not_provided MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN221562|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.542133 0.4058 0.5562 0.5693 0.4651 0.6183 0.3863 0.6311 0.5765 0.5712 0.6279 0.5369 0.4641 0.6383 0.6324 0.3782 0.6205 0.5659 0.6052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 331 1815 chr11 108151707 . T TA 331 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1849;VD=691;AF=0.3737;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.01898;SOR=0.86689;LSEQ=TTTACATTACATTTTTTTTT;RSEQ=AATTTCTTTTTAAGTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1849:691:468,223:668,320:988,691:0.3737:2,2:47.2:1:34.6:1:1:1.01:60:137.2:0.6152:0:0.1 0/1:1815:740:493,247:644,288:932,740:0.4077:2,2:44.4:1:34.8:1:0.29137:1.12025:60:739:0.7161:0.0099:0.1
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chr11 108156049 108156049 T - intronic ATM . . . rs11310321 . . . . . . 0.496006 0.3552 . . . . . . . . . 0.6194 0.7667 0.6559 0.6128 0.3819 0.5727 0.5616 0.6369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 227 240 chr11 108156048 . CT C 227 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=234;VD=91;AF=0.3889;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.34303;SOR=1.09895;LSEQ=TCCAGTATACATTTTTCTCT;RSEQ=TTTTTTTTTTTTGGCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:91:48,43:64,50:114,91:0.3889:2,2:42.4:1:34.9:1:0.67296:1.1459:60:182:0.3889:0.0256:0.1 0/1:240:88:50,38:71,48:119,88:0.3667:2,2:45.5:1:34.8:1:0.77554:1.12353:60:176:0.3667:0.0208:0.1
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chr11 108161554 108161554 A - intronic ATM . . . rs202152959 ID=COSV53756699;OCCURENCE=1(liver) . . . . . . . . . . . . . . . . 0.0247 0.0083 0.0986 0.0531 0 0.2890 0.0135 0.0493 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 233 406 chr11 108161553 . TA T 233 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=350;VD=72;AF=0.2057;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.08115;SOR=0.77217;LSEQ=GAGTGAGACTTTCACTCAAT;RSEQ=AAAAAAAAAAAAAAAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:72:48,24:168,51:219,72:0.2057:2,2:43:1:35:1:0.11966:1.64398:60:144:0.2057:0.0029:0.1 0/1:406:102:76,26:174,51:225,102:0.2512:2,2:43.4:1:35:0:0.57656:1.16661:60:204:0.2512:0:0.1
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chr11 108163323 108163323 - T intron ATM NM_000051:exon30:c.4437-23->T;NM_001351834:exon31:c.4437-23->T . . rs730881290 ID=COSV53726527;OCCURENCE=3(meninges),2(ovary),1(bone) 180460 Hereditary_cancer-predisposing_syndrome MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009 criteria_provided,_single_submitter Benign . . 0.0019 0.0013 0.0003 0.0006 0.0001 0.0012 0.0008 0.0030 0.0043 0.0003 0 0 0 0 0.0015 0.0002 0.0010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 227 1992 chr11 108163323 . G GT 227 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=2016;VD=90;AF=0.0446;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32311;SOR=0.92293;LSEQ=AGAACTTACTGGTTGTTGTT;RSEQ=TTTTTTTTTCTCCCTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2016:90:58,31:1021,613:1634,90:0.0446:2,2:42.7:1:34.3:1:0.65383:1.12:60:89:0.0559:0.004:0.2 0/1:1992:96:53,43:1054,557:1611,96:0.0482:2,2:42:1:34.6:1:0.04747:1.5349:60:192:0.0602:0:0.1
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chr11 108175394 108175394 T C intron ATM NM_000051:exon37:c.5497-8T>C;NM_001351834:exon38:c.5497-8T>C . . rs3092829 ID=COSV53727999;OCCURENCE=1(ovary),3(soft_tissue) 136454 Triple-negative_breast_carcinoma|Malignant_tumor_of_breast|Ataxia-telangiectasia_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0005494,MedGen:C4722518|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.0131789 0.002 0.0246 0.0223 0.0070 0.0166 0.0006 0.0270 0.0335 0.0192 0.0064 0.0220 0.0050 0.0131 0.0199 0.0012 0.0235 0.0338 0.0285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 347 2194 chr11 108175394 . T C 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2275;VD=1094;AF=0.4809;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12997;SOR=0.93313;LSEQ=ATTGGGTGGATTTGTTTGTA;RSEQ=ATTCTAGGTGAAAACTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2275:1094:749,345:779,400:1179,1094:0.4809:2,2:38.8:1:34.4:1:0.22764:1.11:60:83.154:0.4787:0.0097:1.8 0/1:2194:1093:753,340:714,387:1101,1093:0.4982:2,2:38.2:1:34.6:1:0.04603:1.20:60:181.167:0.4968:0.0087:1.8
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chr11 108175462 108175462 G A exonic ATM . nonsynonymous SNV ATM:NM_000051:exon37:c.5557G>A:p.D1853N,ATM:NM_001351834:exon38:c.5557G>A:p.D1853N rs1801516 ID=COSV53728020;OCCURENCE=9(breast),5(meninges),1(large_intestine),10(soft_tissue),2(skin),1(prostate),1(lung),1(testis) 133907 Ataxia-telangiectasia_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.066893 0.0159 0.1023 0.1094 0.0239 0.0523 0.0063 0.2350 0.1456 0.1127 0.0742 0.1113 0.0226 0.0442 0.1424 0.0062 0.2367 0.1457 0.1510 0.197 0.206 T 0.000 0.843 D 0.000 0.520 P 1.82 0.479 L -0.72 0.730 T -1.31 0.328 N -1.062 0.113 T 0.002 0.006 T . . . . . 0.977 0.765 D c 0.163 0.331 1.000 0.747 0.732 0.924 0 5.52 0.821 5.927 0.696 0.998 0.613 1.000 0.715 1.000 0.888 19.804 0.965 . ENSG00000075239.9|ENSG00000075239.9 Muscle_Skeletal|Thyroid 11q22.3 0.5 359 2596 chr11 108175462 . G A 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2664;VD=1317;AF=0.4944;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50412;SOR=0.99905;LSEQ=TTCATGATATTTTACTCCAA;RSEQ=ATACAAATGAATCATGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2664:1317:757,560:754,592:1346,1317:0.4944:2,2:38.2:1:34.7:1:0.45747:1.06:60:187.143:0.4987:0.0169:1.6 0/1:2596:1284:715,569:752,557:1309,1284:0.4946:2,2:38.1:1:34.8:1:0.38339:1.07438:60:427:0.4969:0.0196:1.6
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chr11 108183167 108183167 A G exonic ATM . nonsynonymous SNV ATM:NM_000051:exon40:c.5948A>G:p.N1983S,ATM:NM_001351834:exon41:c.5948A>G:p.N1983S rs659243 ID=COSV53724339;OCCURENCE=18(meninges),2(central_nervous_system),23(upper_aerodigestive_tract) 137366 Ataxia-telangiectasia_syndrome|not_specified|not_provided MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 1 1 . 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 1 375 1847 chr11 108183167 . A G 375 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1765;VD=1759;AF=0.9966;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46926;SOR=0.79584;LSEQ=ATTTGAAGAAGGAAGCCAGA;RSEQ=TACAACTATTTCTAGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1765:1759:1093,666:1,0:1,1759:0.9966:0,2:39.8:1:34.4:1:1:0:60:134.308:0.9989:0.0187:1.1 1/1:1847:1842:1194,648:1,0:1,1842:0.9973:0,2:39.9:1:34.6:1:1:0:60:107.353:0.9989:0.0168:1.1
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chr11 108188266 108188266 - T intron ATM NM_000051:exon43:c.6347+18->T;NM_001351834:exon44:c.6347+18->T . . rs752198015 ID=COSV53736193;OCCURENCE=1(breast),1(liver) 1199991 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 no_assertion_criteria_provided Benign/Likely_benign . . 0.0452 0.0458 0.0158 0.0547 0.0513 0.0278 0.0484 0.0256 0.0547 0.0013 0.0007 0.0056 0 0.0007 0.0010 0.0016 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 246 1198 chr11 108188266 . A AT 246 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1188;VD=139;AF=0.117;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.25582;SOR=1.09802;LSEQ=CAGGTAAGAAATTTGACTTG;RSEQ=TTTTTTTTTTTTTGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1188:139:57,82:244,498:742,139:0.117:2,2:47.9:1:34.6:1:0.07909:1.42:60:138:0.1885:0:0.1 0/1:1198:129:46,83:293,531:824,129:0.1077:2,2:48.5:1:34.5:1:1:1.00:60:128:0.1565:0:0.1
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chr11 108195977 108195977 T - intronic ATM;C11orf65 . . . rs11366542 . 1242251 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.725639 0.7778 . . . . . . . . . 0.5815 0.4518 0.6596 0.6667 0.7413 0.4696 0.6454 0.6438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 274 479 chr11 108195976 . GT G 274 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=540;VD=254;AF=0.4704;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.04334;SOR=0.80019;LSEQ=TAAGTTCCAGAACTTACATA;RSEQ=TTTTTTTTTTTTTTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:254:182,72:105,52:157,254:0.4704:2,2:35.3:1:34.4:1:0.32091:1.25:60:253:0.472:0.0519:0.2 1/0:479:252:179,73:94,32:126,252:0.5261:2,2:35.2:1:34.5:1:0.54267:1.19741:60:504:0.5294:0.0814:0.2
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chr11 108196957 108196957 - T intron ATM NM_000051:exon47:c.6975+5->T;NM_001351834:exon48:c.6975+5->T . . rs763287238 ID=COSV53759063;OCCURENCE=1(meninges),1(skin) 222106 Malignant_tumor_of_breast|Ataxia-telangiectasia_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . . 8.492e-05 0 0 0.0001 0.0003 9.222e-05 0.0014 0 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 166 1913 chr11 108196957 . G GT 166 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1927;VD=27;AF=0.014;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.48909;SOR=0.95667;LSEQ=TGCCAGCTGTGCAGCGGTTT;RSEQ=TTTTTTTTATTGGCTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1927:27:9,17:796,1014:1810,27:0.014:2,2:43.8:1:35:1:0.42727:1.48249:60:54:0.0153:0.001:0 0/1:1913:28:11,16:803,992:1795,28:0.0146:2,2:41.2:1:34.6:1:0.70232:1.17731:60:56:0.0157:0:0
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chr11 108203632 108203632 - T intron ATM NM_000051:exon53:c.7927+5->T;NM_001351834:exon54:c.7927+5->T . . rs587781324 ID=COSV53726414;OCCURENCE=1(stomach),3(large_intestine),1(biliary_tract) 150571 Ataxia-telangiectasia_syndrome|Hereditary_cancer-predisposing_syndrome|Familial_ovarian_cancer|not_specified|not_provided MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016248,MedGen:CN201036,Orphanet:ORPHA213517|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . 0.0003 0.0002 0.0002 9.038e-05 0.0001 0 0.0002 0 0.0002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.25 136 1439 chr11 108203632 . G GT 136 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1423;VD=15;AF=0.0105;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06283;SOR=2.1788;LSEQ=TGGAAGACTCAGAGAAGTAT;RSEQ=TTTTTTTTAAAGAAGAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1423:15:7,8:640,703:1343,15:0.0105:2,2:49.5:1:35:0:1:1.04042:60:30:0.0115:0:0.1 0/0:1439:7:4,3:640,663:1303,7:0.0049:2,2:32.7:1:35:1:0.72155:1.38:60:14:0.0054:0.0007:0.1
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chr11 108236783 108236783 G T UTR3 ATM NM_000051:c.*548G>T;NM_001351834:c.*548G>T . . rs227092 . 324952 Ataxia-telangiectasia_syndrome MONDO:MONDO:0008840,MedGen:C0004135,OMIM:208900,Orphanet:ORPHA100,SNOMED_CT:68504005 criteria_provided,_single_submitter Benign 0.518371 0.4345 . . . . . . . . . 0.5152 0.3817 0.6472 0.62 0.4141 0.6368 0.5633 0.6112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q22.3 0.5 312 1285 chr11 108236783 . G T 312 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1289;VD=553;AF=0.429;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22814;SOR=0.93956;LSEQ=AAAAAAAAAAAAACAGAAAC;RSEQ=TATTTGGATTTTTCCTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1289:553:381,172:464,270:734,553:0.429:2,2:42:1:34:1:0.03791:1.29:60:49.273:0.4367:0.0031:1.2 0/1:1285:571:384,187:426,285:711,571:0.4444:2,2:40.2:1:34.1:1:0.00736:1.37:60:50.909:0.4512:0.0101:1.2
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chr11 125505377 125505377 - A exonic CHEK1 . frameshift insertion CHEK1:NM_001330427:exon6:c.716dupA:p.T242Nfs*19,CHEK1:NM_001330428:exon6:c.386dupA:p.T132Nfs*19,CHEK1:NM_001114121:exon7:c.668dupA:p.T226Nfs*19,CHEK1:NM_001114122:exon7:c.668dupA:p.T226Nfs*19,CHEK1:NM_001244846:exon7:c.668dupA:p.T226Nfs*19,CHEK1:NM_001274:exon7:c.668dupA:p.T226Nfs*19 rs757716680 ID=COSV54022229;OCCURENCE=1(meninges),4(large_intestine),1(biliary_tract),4(NS),1(stomach),1(small_intestine) . . . . . . . . 0.0005 0.0003 0 0.0001 0.0002 0.0004 0 0.0016 3.567e-05 0 0 0 0 0 7.361e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q24.2 0.5 194 1617 chr11 125505377 . G GA 194 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1713;VD=47;AF=0.0274;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16705;SOR=1.27505;LSEQ=AGGAGTATTCTGACTGGAAA;RSEQ=AAAAAAAAACATACCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1713:47:24,23:946,632:1578,47:0.0274:2,2:44.8:1:35:0:0.23025:1.43411:60:94:0.0306:0:0.1 0/1:1617:35:23,12:834,584:1418,35:0.0216:2,2:40.9:1:34.7:1:0.48824:1.34:60:70:0.0251:0.0019:0.1
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chr11 125514573 125514573 G A intron CHEK1 NM_001114122:exon11:c.1233+35G>A;NM_001244846:exon11:c.1233+35G>A;NM_001114121:exon11:c.1233+35G>A;NM_001330427:exon10:c.1281+35G>A;NM_001330428:exon10:c.951+35G>A;NM_001274:exon11:c.1233+35G>A . . rs521102 . . . . . . 0.436102 0.4058 0.4365 0.5076 0.2804 0.6343 0.3929 0.4906 0.5148 0.5087 0.5815 0.4490 0.2798 0.6340 0.5629 0.3717 0.4989 0.5276 0.5051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11q24.2 0.5 339 1732 chr11 125514573 . G A 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1727;VD=850;AF=0.4922;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29975;SOR=1.03878;LSEQ=TTTTCATTATACCTTTTCCT;RSEQ=AAGAAGAATTTAAATATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1727:850:403,447:423,452:875,850:0.4922:2,2:41:1:34.9:1:0.7001:1.03802:60:849:0.4945:0.0017:1.1 0/1:1732:836:386,450:408,487:895,836:0.4827:2,2:39.5:1:34.9:1:0.80951:1.02:60:417:0.4849:0.015:1.1
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chr11 125525195 125525195 A G exonic CHEK1 . nonsynonymous SNV CHEK1:NM_001244846:exon12:c.1309A>G:p.I437V,CHEK1:NM_001330427:exon12:c.1459A>G:p.I487V,CHEK1:NM_001330428:exon12:c.1129A>G:p.I377V,CHEK1:NM_001114121:exon13:c.1411A>G:p.I471V,CHEK1:NM_001114122:exon13:c.1411A>G:p.I471V,CHEK1:NM_001274:exon13:c.1411A>G:p.I471V rs506504 . 487497 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.985823 1 0.9738 0.9732 0.9956 0.9850 0.9996 0.9646 0.9621 0.9568 0.9812 0.9774 0.9928 0.9761 0.9603 1 0.9694 0.9683 0.9776 1.0 0.010 T 0.001 0.425 N 1.000 0.090 P -1.155 0.009 N -0.5 0.707 T 0.38 0.036 N -0.951 0.408 T 0.000 0.000 T . . . . . 0.128 0.173 N c -0.900 -0.642 0.015 0.127 0.707 0.730 0 1.8 0.240 1.211 0.318 -0.223 0.096 1.000 0.715 0.993 0.574 2.296 0.039 . . . 11q24.2 1 372 1849 chr11 125525195 . A G 372 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1845;VD=1841;AF=0.9978;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49881;SOR=0.74803;LSEQ=ATATTGTGAGCAGCCAGAAG;RSEQ=TTTGGCTTCCTGCCACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1845:1841:970,871:0,0:0,1841:0.9978:0,2:41.1:1:34.2:1:1:0:60:60.367:0.9994:0.0179:1.1 1/1:1849:1846:1002,844:1,0:1,1846:0.9984:0,2:40.9:1:34.3:1:1:0:60:79.261:0.9995:0.0195:1.1
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chr12 4388084 4388084 C G exonic CCND2 . synonymous SNV CCND2:NM_001759:exon3:c.570C>G:p.T190T rs3217805 ID=COSV54221448;OCCURENCE=7(meninges),14(soft_tissue),1(lung) 375127 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus_syndrome_3|not_specified MONDO:MONDO:0014408,MedGen:C4014742,OMIM:615938|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.219848 0.0833 0.3263 0.3182 0.1863 0.2912 0.0875 0.3555 0.3920 0.2994 0.2615 0.3148 0.1994 0.3019 0.4669 0.0619 0.3546 0.3950 0.3551 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12p13.32 0.5 348 2236 chr12 4388084 . C G 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2235;VD=1114;AF=0.4984;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3323;SOR=1.02812;LSEQ=TTCATTGCTCTGTGTGCCAC;RSEQ=GGTAAGATGAGGCTTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2235:1114:527,587:515,601:1116,1114:0.4984:2,2:40.3:1:34.4:1:0.61054:1.05:60:73.267:0.498:0.0139:1.1 0/1:2236:1099:553,546:552,577:1129,1099:0.4915:2,2:38.9:1:34.6:1:0.52502:1.06:60:182.167:0.4937:0.0165:1.1
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chr12 21331599 21331599 T C exonic SLCO1B1 . synonymous SNV SLCO1B1:NM_006446:exon6:c.571T>C:p.L191L rs4149057 ID=COSV57008088;OCCURENCE=1(breast),2(large_intestine),1(haematopoietic_and_lymphoid_tissue),3(lung) 254472 Rotor_syndrome|not_specified|not_provided MONDO:MONDO:0009379,MedGen:C0220991,OMIM:237450,Orphanet:ORPHA3111,SNOMED_CT:32891000|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.367412 0.2431 0.4881 0.5232 0.1979 0.5162 0.2518 0.5130 0.6196 0.4855 0.5240 0.4538 0.2051 0.5287 0.6424 0.2478 0.5014 0.5976 0.5194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12p12.1 0.5 309 1058 chr12 21331599 . T C 309 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1072;VD=511;AF=0.4767;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28999;SOR=0.94961;LSEQ=GGGAGACTCCCATAGTACCA;RSEQ=TGGGGCTTTCTTACATTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1072:511:317,194:361,198:559,511:0.4767:2,2:42.8:1:34.4:1:0.40915:1.11568:60:101.2:0.4756:0.0047:1.1 0/1:1058:518:339,179:336,202:538,518:0.4896:2,2:41:1:34.3:1:0.33642:1.14:60:73:0.4881:0.0132:1.1
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chr12 21331625 21331625 C T exonic SLCO1B1 . synonymous SNV SLCO1B1:NM_006446:exon6:c.597C>T:p.F199F rs2291075 ID=COSV57010363;OCCURENCE=1(large_intestine),1(stomach),1(skin) 254473 Rotor_syndrome|not_specified|not_provided MONDO:MONDO:0009379,MedGen:C0220991,OMIM:237450,Orphanet:ORPHA3111,SNOMED_CT:32891000|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.415535 0.5109 0.4489 0.3791 0.5554 0.2474 0.5075 0.4585 0.4029 0.4179 0.1977 0.4524 0.5550 0.2843 0.42 0.5262 0.4630 0.3967 0.3865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12p12.1 0.5 315 1048 chr12 21331625 . C T 315 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1047;VD=528;AF=0.5043;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50879;SOR=0.99811;LSEQ=CTTTCTTACATTGATGATTT;RSEQ=GCTAAAGAAGGACATTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1047:528:291,237:298,221:519,528:0.5043:2,2:43.7:1:35:1:0.45548:1.0981:60:1056:0.5067:0.0038:1.5 1/0:1048:529:293,236:302,217:519,529:0.5048:2,2:44.3:1:34.9:1:0.38276:1.12084:60:528:0.5062:0.0057:1.6
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chr12 25368462 25368462 C T exonic KRAS . synonymous SNV KRAS:NM_001369786:exon5:c.483G>A:p.R161R,KRAS:NM_033360:exon5:c.483G>A:p.R161R rs4362222 ID=COSV55501936;OCCURENCE=18(meninges),42(large_intestine),2(central_nervous_system),1(lung) 55703 Noonan_syndrome_3|Rasopathy|not_specified|not_provided MONDO:MONDO:0012371,MedGen:C1860991,OMIM:609942|MONDO:MONDO:0021060,MedGen:CN166718,Orphanet:ORPHA536391|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.997604 1 0.9985 0.9995 0.9945 0.9997 1 1 1 1 1 0.9985 0.9948 1 1 1 1 1 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12p12.1 1 370 1596 chr12 25368462 . C T 370 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1560;VD=1555;AF=0.9968;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30464;SOR=1.56652;LSEQ=AATCTGTATTGTCGGATCTC;RSEQ=CTCACCAATGTATAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1560:1555:632,923:0,0:0,1555:0.9968:0,2:40.9:1:34.8:1:1:0:60:387.75:0.9974:0.0333:1.1 1/1:1596:1588:660,928:0,0:0,1588:0.995:0,2:42.8:1:34.8:1:1:0:60:396:0.9981:0.0132:1.1
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chr12 56477694 56477694 A T intron ERBB3 NM_001982:exon2:c.234+8A>T;NM_001005915:exon2:c.234+8A>T . . rs2271194 ID=COSV57265950;OCCURENCE=1(breast),2(central_nervous_system) 1245322 Lethal_congenital_contracture_syndrome_2|Visceral_neuropathy,_familial|not_provided MONDO:MONDO:0011868,MedGen:C1843478,OMIM:607598,Orphanet:ORPHA137776|MONDO:MONDO:0023961,MedGen:C1855733,OMIM:PS243180|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.592252 0.7808 0.4955 0.6214 0.3135 0.7931 0.7861 0.6005 0.5871 0.6326 0.7171 0.5370 0.3344 0.7279 0.5199 0.7841 0.5922 0.6002 0.6074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q13.2 0.5 358 2488 chr12 56477694 . A T 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2521;VD=1262;AF=0.5006;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31954;SOR=1.02851;LSEQ=CTCCTTCCTGCAGGTTAGTG;RSEQ=GCCCACCCTCCTTCCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2521:1262:508,754:541,714:1255,1262:0.5006:2,2:41.4:1:34.8:1:0.15705:1.12457:60:1261:0.5103:0.0186:1.1 0/1:2488:1228:484,744:490,756:1246,1228:0.4936:2,2:40:1:34.7:1:0.9672:1.00:60:135.444:0.5002:0.0181:1.1
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chr12 56493822 56493822 A C intron ERBB3 NM_001982:exon25:c.3129+9A>C . . rs2292238 ID=COSV57256344;OCCURENCE=2(breast),77(meninges),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 1214779 Lethal_congenital_contracture_syndrome_2|Visceral_neuropathy,_familial|not_provided MONDO:MONDO:0011868,MedGen:C1843478,OMIM:607598,Orphanet:ORPHA137776|MONDO:MONDO:0023961,MedGen:C1855733,OMIM:PS243180|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.295128 0.3214 0.3357 0.3600 0.1861 0.3803 0.3490 0.3864 0.4051 0.3718 0.2865 0.3482 0.1849 0.3914 0.4834 0.3468 0.3983 0.4231 0.4012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q13.2 0.5 349 2417 chr12 56493822 . A C 349 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2467;VD=1216;AF=0.4929;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48091;SOR=0.99563;LSEQ=CGGCCACGTGGGGTAAGACA;RSEQ=CTTCTAATTACCCAACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2467:1216:656,560:648,594:1242,1216:0.4929:2,2:40.1:1:34.1:1:0.39603:1.07:60:63:0.4908:0.0126:1.1 0/1:2417:1194:630,564:640,577:1217,1194:0.494:2,2:38.3:1:34.2:1:0.93502:1.01:60:65.333:0.4923:0.0182:1.1
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chr12 56494991 56494991 G A exonic ERBB3 . synonymous SNV ERBB3:NM_001982:exon27:c.3348G>A:p.R1116R rs2271189 ID=COSV57251880;OCCURENCE=1(breast),75(meninges),2(central_nervous_system),1(stomach),3(lung) 1238955 Lethal_congenital_contracture_syndrome_2|Visceral_neuropathy,_familial|not_provided MONDO:MONDO:0011868,MedGen:C1843478,OMIM:607598,Orphanet:ORPHA137776|MONDO:MONDO:0023961,MedGen:C1855733,OMIM:PS243180|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.252196 0.2887 0.3101 0.3396 0.1224 0.3587 0.3242 0.3836 0.3955 0.3473 0.2508 0.3256 0.1251 0.3744 0.4195 0.3222 0.3949 0.4180 0.3857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q13.2 0.5 370 3064 chr12 56494991 . G A 370 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3242;VD=1674;AF=0.5163;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13195;SOR=1.05924;LSEQ=GAGAAAGTGTCAATGTGTAG;RSEQ=AGCCGGAGCAGGAGCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3242:1674:1074,600:949,615:1564,1674:0.5163:2,2:37.4:1:34.6:1:0.04203:1.16:60:208.25:0.5171:0.0185:1.1 1/0:3064:1538:933,605:944,578:1522,1538:0.502:2,2:39.2:1:34.6:1:0.45783:1.05901:60:169.889:0.5033:0.0189:1.1
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chr12 58142005 58142005 A - UTR3 CDK4;TSPAN31 NM_000075:c.*303delT;NM_005981:c.*932delA;NM_001330169:c.*932delA;NM_001330168:c.*932delA . . rs59185470 . 332311 Cutaneous_Malignant_Melanoma,_Dominant MedGen:CN239351 criteria_provided,_single_submitter Uncertain_significance . . . . . . . . . . . 0.0704 0.1609 0.0795 0.0333 0.0060 0.1968 0.0118 0.0525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q14.1 0.5 277 1138 chr12 58142004 . TA T 277 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1164;VD=247;AF=0.2122;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.08139;SOR=1.16294;LSEQ=CCAAACAGAGGAAGAAACAT;RSEQ=AAAAAAAAAAAAAGACCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1164:247:143,104:450,391:841,247:0.2122:2,2:45.3:1:34.9:1:0.24502:1.19:60:494:0.2127:0.006:0.1 0/1:1138:214:116,98:445,402:847,214:0.188:2,2:45.3:1:34.9:1:0.70174:1.07:60:428:0.1889:0.0105:0.1
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chr12 58144350 58144350 A - intronic CDK4 . . . rs751112756 ID=COSV56985421;OCCURENCE=2(large_intestine) . . . . . . . . 0.0017 0.0014 0.0019 0.0014 0.0010 0.0017 0 0.0024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q14.1 0.5 235 2269 chr12 58144349 . CA C 235 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2430;VD=108;AF=0.0444;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.04487;SOR=1.30642;LSEQ=AACACAGCAAGCCCTGGTCT;RSEQ=AAAAAAAAGAATGGGCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2430:108:68,40:1579,735:2314,108:0.0444:2,2:40.2:1:34.9:1:0.2477:1.26354:60:216:0.0444:0.0062:0.2 0/1:2269:78:61,17:1462,724:2186,78:0.0344:2,2:38.2:1:34.9:1:0.03694:1.78:60:156:0.0344:0.004:0.2
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chr12 58145156 58145156 C T intron CDK4 NM_000075:exon3:c.219-31G>A . . rs2270777 ID=COSV56985436;OCCURENCE=1(lung) 1238187 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.248003 0.1776 0.3478 0.3302 0.1644 0.2105 0.1493 0.3602 0.4325 0.3833 0.2364 0.3299 0.1680 0.2770 0.5 0.1667 0.3642 0.4307 0.3704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q14.1 0.5 364 2807 chr12 58145156 . C T 364 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2815;VD=1384;AF=0.4917;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.15449;SOR=1.05728;LSEQ=TAAATGCTCACTTTTCAATC;RSEQ=CCTTTAACCCAACATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2815:1384:658,726:647,778:1425,1384:0.4917:2,2:39.8:1:34.9:1:0.25666:1.09:60:691:0.4961:0.0199:1.1 0/1:2807:1341:592,749:634,827:1461,1341:0.4777:2,2:40.7:1:34.6:1:0.70314:1.03:60:190.571:0.483:0.0143:1.1
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chr12 69214081 69214081 - T intron MDM2 NM_001145339:exon5:c.309-24->T;NM_002392:exon5:c.309-24->T;NM_001367990:exon5:c.291-24->T;NM_001145337:exon5:c.291-24->T . . rs773714225 ID=COSV104382808;OCCURENCE=1(meninges) . . . . . . . 0.1132 0.1948 0.1904 0.2093 0.1774 0.0784 0.1879 0.2302 0.2625 0.0032 0.0017 0.0137 0.0081 0 0.0143 0.0025 0.0066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q15 0.5 252 1301 chr12 69214081 . A AT 252 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1326;VD=135;AF=0.1018;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.09783;SOR=0.84429;LSEQ=TAAAATGTACATCTCTTGTT;RSEQ=TTTTTTTTTTTTCTGTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1326:135:88,47:588,353:941,135:0.1018:2,2:43.1:1:34.3:1:0.56899:1.12:60:66.5:0.1424:0.0008:0.2 0/1:1301:154:107,47:581,332:913,154:0.1184:2,2:36.9:1:34.8:1:0.17278:1.30:60:308:0.1692:0.0215:0.1
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chr12 69229771 69229771 T - intron MDM2 NM_001145339:exon7:c.675+7T>-;NM_002392:exon9:c.840+7T>-;NM_001367990:exon9:c.822+7T>-;NM_001278462:exon4:c.312+7T>-;NM_001145340:exon4:c.312+7T>- . . rs533467429 ID=COSV50697907;OCCURENCE=5(stomach),1(upper_aerodigestive_tract),3(large_intestine) . . . . . 0.00119808 0.002 0.0016 0.0005 0.0002 0.0011 0.0006 0 0.0006 0.0015 0.0003 0.0003 0.0002 0.0024 0 0.0006 0 0.0003 0.0010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q15 0.25 153 1770 chr12 69229770 . AT A 153 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=1722;VD=17;AF=0.0099;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28894;SOR=0.79227;LSEQ=GATGAAGATGATGAGGTAGT;RSEQ=TTTTTTTCCCCTCTAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1722:17:6,11:858,846:1704,17:0.0099:2,2:48.9:1:35:0:0.23381:1.85867:60:34:0.0099:0:0.2 0/1:1770:22:9,13:862,886:1748,22:0.0124:2,2:38.9:1:34.5:1:0.52201:1.40504:60:44:0.0125:0.0006:0
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chr12 133202215 133202215 G A intron POLE NM_006231:exon47:c.6657+16C>T . . rs5745075 ID=COSV57683709;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) 358843 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.423323 0.6657 0.3203 0.3771 0.3667 0.5064 0.7041 0.4111 0.3038 0.3507 0.3675 0.3590 0.3566 0.4726 0.19 0.6983 0.4014 0.3111 0.3561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 0.5 359 2581 chr12 133202215 . G A 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2500;VD=1242;AF=0.4968;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49753;SOR=1.00192;LSEQ=TCCAGGGCACACGGGCAGGC;RSEQ=GCATGCACGACTCACCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2500:1242:800,442:846,403:1249,1242:0.4968:2,2:39.6:1:34.9:1:0.0828:1.15977:60:1241:0.5:0.0116:1.1 0/1:2581:1281:833,448:884,400:1284,1281:0.4963:2,2:39.1:1:34.8:1:0.04391:1.18849:60:255.2:0.499:0.019:1.1
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chr12 133208886 133208886 C T intron POLE NM_006231:exon45:c.6330+15G>A . . rs5745023 . 374673 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.565096 0.6736 0.4803 0.4993 0.5855 0.5800 0.7119 0.4510 0.4284 0.4925 0.5467 0.4931 0.5854 0.5813 0.3775 0.7048 0.4327 0.4301 0.4611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 386 2243 chr12 133208886 . C T 386 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2156;VD=2139;AF=0.9921;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.35764;SOR=1.1891;LSEQ=GTGTCCTCTCCTCACACGCA;RSEQ=GCTGGCACTCTCACCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2156:2139:1416,723:0,0:0,2139:0.9921:0,2:39.7:1:34.8:1:1:0:60:304.571:0.9949:0.0083:1.6 1/1:2243:2222:1503,719:1,0:1,2222:0.9906:0,2:39.6:1:34.8:1:1:0:60:369.333:0.9937:0.0236:1.6
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chr12 133208979 133208979 T C exonic POLE . synonymous SNV POLE:NM_006231:exon45:c.6252A>G:p.S2084S rs5745022 . 371896 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Hereditary_cancer-predisposing_syndrome|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.699081 0.7788 0.6427 0.6421 0.7643 0.8004 0.8146 0.5884 0.5818 0.6110 0.6065 0.6546 0.7676 0.7685 0.5099 0.8075 0.5790 0.5901 0.5992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 401 3060 chr12 133208979 . T C 401 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3181;VD=3171;AF=0.9969;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55374;SOR=1.03968;LSEQ=GGGAGGACAGGAAACATCTC;RSEQ=GAGAGCTCAGTGGAGTTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3181:3171:1929,1242:0,0:0,3171:0.9969:0,2:39.4:1:34.5:1:1:0:60:143.136:0.9984:0.0374:1.4 1/1:3060:3050:1867,1183:0,1:1,3050:0.9967:0,2:38.8:1:34.5:1:0.38807:0:60:144.238:0.9984:0.0438:1.4
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chr12 133210985 133210985 C T intron POLE NM_006231:exon43:c.5812-21G>A . . rs5745005 . 665510 Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_provided MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.713458 0.7788 0.6565 0.6493 0.8077 0.8032 0.8141 0.5878 0.5837 0.6170 0.6174 0.6669 0.8091 0.7727 0.5099 0.8080 0.5793 0.5909 0.6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 373 1929 chr12 133210985 . C T 373 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1948;VD=1938;AF=0.9949;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.32969;SOR=1.31483;LSEQ=CTGTAACACATGAGACAACG;RSEQ=GGCTGTGTTTGCACCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1948:1938:638,1300:0,0:0,1938:0.9949:0,2:41.5:1:34.2:1:1:0:60:70.778:0.9969:0.0262:1.1 1/1:1929:1916:569,1347:0,0:0,1916:0.9933:0,2:41.8:1:34.7:1:1:0:60:211.889:0.9963:0.0306:1.1
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chr12 133214768 133214768 A G intron POLE NM_006231:exon41:c.5553-43T>C . . rs5744970 . 666205 Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_provided MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.729034 0.7788 0.6748 0.6519 0.8614 0.8064 0.8144 0.5882 0.5830 0.6173 0.6072 0.6803 0.8569 0.7739 0.5067 0.8073 0.5791 0.5908 0.6035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 372 1710 chr12 133214768 . A G 372 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1659;VD=1647;AF=0.9928;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53058;SOR=1.05142;LSEQ=GTGGTGGAGACGCCACAGTC;RSEQ=TGGAGAGCCAGAGGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1659:1647:767,880:3,2:5,1647:0.9928:2,2:42.5:1:34.7:1:0.66893:1.72041:60:234.286:0.9945:0.0313:1.1 1/1:1710:1697:742,955:2,2:4,1697:0.9924:2,2:42.5:1:34.7:1:1:1.28686:60:187.556:0.9924:0.007:1.1
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chr12 133219831 133219831 T C exonic POLE . synonymous SNV POLE:NM_006231:exon35:c.4530A>G:p.A1510A rs5744944 ID=COSV57686501;OCCURENCE=1(lung),1(thyroid) 372706 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Hereditary_cancer-predisposing_syndrome|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.605232 0.6736 0.5224 0.5078 0.7153 0.5834 0.7107 0.4409 0.4258 0.4899 0.5441 0.5291 0.7113 0.5897 0.3733 0.7043 0.4335 0.4301 0.4684 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 384 2346 chr12 133219831 . T C 384 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2391;VD=2379;AF=0.995;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16658;SOR=1.53271;LSEQ=GTGTCCAGCACAAAGACGGA;RSEQ=GCCCTGCGCTGTGAGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2391:2379:1512,867:0,1:1,2379:0.995:0,2:40.3:1:34.3:1:0.36471:0:60:94.16:0.9979:0.0201:1.1 1/1:2346:2328:1486,842:2,0:2,2328:0.9923:0,2:40.9:1:34.4:1:0.53824:0:60:128.333:0.9957:0.0068:1.1
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chr12 133220099 133220100 CA - exonic POLE . frameshift deletion POLE:NM_006231:exon34:c.4337_4338del:p.V1446Gfs*3 rs758487568 ID=COSV57674558;OCCURENCE=1(meninges),10(large_intestine),8(NS),1(urinary_tract) 399202 Colorectal_cancer,_susceptibility_to,_12|Hereditary_cancer-predisposing_syndrome MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009 criteria_provided,_multiple_submitters,_no_conflicts Uncertain_significance . . . 2.825e-05 0.0001 0 0 0 0 0 0.0001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 0.5 198 3141 chr12 133220098 . CCA C 198 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3297;VD=53;AF=0.0161;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.1824;SOR=1.23526;LSEQ=CCTCACCAGCTGTTTATTGA;RSEQ=CACACACACAGCCCAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3297:53:25,28:1853,1389:3242,53:0.0161:2,2:35.5:1:34.6:1:0.16246:1.49393:60:106:0.0162:0.0024:0.1 0/1:3141:41:23,18:1800,1300:3100,41:0.0131:2,2:37.6:1:34.9:1:0.87378:1.08358:60:82:0.0131:0.0019:0.3
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chr12 133220526 133220526 T C exonic POLE . nonsynonymous SNV POLE:NM_006231:exon33:c.4187A>G:p.N1396S rs5744934 ID=COSV57680345;OCCURENCE=1(large_intestine),1(lung),1(thyroid) 374712 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Hereditary_cancer-predisposing_syndrome|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.120607 0.0089 0.1357 0.1162 0.1437 0.0679 0.0067 0.0384 0.1273 0.1354 0.1800 0.1151 0.1499 0.1053 0.1887 0.0068 0.0389 0.1243 0.1031 0.023 0.481 D 0.001 0.416 D 0.062 0.372 P 2.395 0.694 M 2.1 0.200 T -3.34 0.663 D -1.099 0.043 T 0.000 0.001 T . . . . . 0.974 0.741 D c 0.156 0.292 1.000 0.747 0.707 0.730 0 5.51 0.817 4.747 0.616 1.061 0.807 1.000 0.715 1.000 0.888 14.525 0.673 . ENSG00000247077.2 Cells_Transformed_fibroblasts 12q24.33 0.5 367 3035 chr12 133220526 . T C 367 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2976;VD=1462;AF=0.4913;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06921;SOR=0.92517;LSEQ=GCACTGAATACTCATAGAGA;RSEQ=TGTAGACCATGTTGGAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2976:1462:780,682:796,712:1508,1462:0.4913:2,2:38.8:1:34.6:1:0.76868:1.02:60:145.2:0.4902:0.0034:1.1 1/0:3035:1550:816,734:763,717:1480,1550:0.5107:2,2:38.2:1:34.7:1:0.56062:1.04:60:192.75:0.5103:0.0161:1.2
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chr12 133233705 133233705 T C intron POLE NM_006231:exon29:c.3582+17A>G . . rs5744889 . 374780 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.983826 1 0.9729 0.9714 0.9917 0.9734 0.9997 0.9643 0.9656 0.9697 0.9669 0.9764 0.9929 0.9749 0.9868 1 0.9625 0.9678 0.9694 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 381 2033 chr12 133233705 . T C 381 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2113;VD=2099;AF=0.9934;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.54043;SOR=0.96489;LSEQ=GATCCCGCCCAGCCCAGCCT;RSEQ=GGGGCCCCACCGTCACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2113:2099:1393,706:1,0:1,2099:0.9934:0,2:37.9:1:34.6:1:1:0:60:138.933:0.9947:0.0099:1.1 1/1:2033:2020:1363,657:2,1:3,2020:0.9936:2,2:37.9:1:34.6:1:1:1.04:60:223.444:0.9951:0:1.1
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chr12 133236000 133236000 C T exonic POLE . synonymous SNV POLE:NM_006231:exon26:c.3156G>A:p.T1052T rs5744857 . 372744 Colorectal_cancer,_susceptibility_to,_12|Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Hereditary_cancer-predisposing_syndrome|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.605431 0.6736 0.5225 0.5077 0.7150 0.5830 0.7105 0.4401 0.4259 0.4885 0.5437 0.5300 0.7123 0.5935 0.3885 0.7048 0.4338 0.4309 0.4682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 406 3188 chr12 133236000 . C T 406 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3153;VD=3145;AF=0.9975;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49132;SOR=0.86512;LSEQ=CGCTTTGCTGTGCTGATGGA;RSEQ=GTAGACTTCTGCTCCCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3153:3145:1671,1474:1,0:1,3145:0.9975:0,2:39.8:1:34.8:1:1:0:60:348.444:0.9981:0.0257:1.1 1/1:3188:3181:1787,1394:1,1:2,3181:0.9978:2,2:40.7:1:34.9:1:1:1.28:60:1059.333:0.9978:0.0104:1.1
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chr12 133237754 133237754 A - intron POLE NM_006231:exon25:c.2865-4T>- . . rs369732588 ID=COSV57673646;OCCURENCE=1(large_intestine),4(biliary_tract),4(skin) 685310 Colorectal_cancer,_susceptibility_to,_12|not_specified|not_provided MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign . . . 0.4535 0.4331 0.4656 0.4469 0.4636 0.4606 0.4630 0.4225 0.0417 0.0118 0.1627 0.0385 0.0020 0.1273 0.0528 0.0557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 0.5 300 2350 chr12 133237753 . GA G 300 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2420;VD=391;AF=0.1616;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.49479;SOR=0.9959;LSEQ=TCATTGAACACAGCATACCT;RSEQ=AAAAAAAAAAAAAGGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2420:391:177,214:809,1022:1831,391:0.1616:2,2:44.5:1:34.9:1:0.69515:1.04:60:782:0.162:0.0087:0.1 0/1:2350:381:172,209:792,979:1771,381:0.1621:2,2:46.3:1:34.9:1:0.90961:1.02:60:762:0.1629:0.0064:0.2
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chr12 133238076 133238076 T C intron POLE NM_006231:exon24:c.2864+37A>G . . rs5744844 . 1273129 Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_provided MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.577276 0.6736 0.4927 0.5006 0.6244 0.5784 0.7107 0.4403 0.4263 0.4840 0.5498 0.5058 0.6288 0.5837 0.38 0.7057 0.4338 0.4303 0.4644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 383 2174 chr12 133238076 . T C 383 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2217;VD=2204;AF=0.9941;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20368;SOR=0.62625;LSEQ=ATTTAATCTATCTCAATCCA;RSEQ=GTCCTTTCTAAAGCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2217:2204:1430,774:4,2:6,2204:0.9941:2,2:40.1:1:34.5:1:1:1.08249:60:115:0.9954:0.0059:1.1 1/1:2174:2166:1370,796:1,0:1,2166:0.9963:0,2:40.2:1:34.6:1:1:0:60:165.615:0.9981:0.034:1.1
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chr12 133240782 133240782 A G intron POLE NM_006231:exon23:c.2562-48T>C . . rs4883592 ID=COSV57673785;OCCURENCE=1(large_intestine),1(stomach) 666357 Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_provided MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.605831 0.6756 0.5226 0.5099 0.7159 0.5876 0.7126 0.4414 0.4278 0.4898 0.5460 0.5278 0.7128 0.5888 0.3810 0.7035 0.4295 0.4270 0.4619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 368 2361 chr12 133240782 . A G 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2403;VD=2378;AF=0.9896;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00511;SOR=0.36403;LSEQ=TGAGTTCCCCTTTCCTTTTC;RSEQ=CCCAGTGTGTGGCCTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2403:2378:1098,1280:2,5:7,2378:0.9896:2,2:42.6:1:32.9:1:0.46228:2.14:60:27.31:0.9939:0:1.1 1/1:2361:2352:1053,1299:1,2:3,2352:0.9962:2,2:40.7:1:33:1:1:1.62:60:21.835:0.9982:0.0288:1.2
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chr12 133249274 133249274 C - exonic POLE . frameshift deletion POLE:NM_006231:exon15:c.1625delG:p.G542Afs*21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 0.25 164 2554 chr12 133249273 . GC G 164 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2513;VD=26;AF=0.0103;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.31169;SOR=1.20316;LSEQ=GACTCGAGGGCCTCCACGTG;RSEQ=CCCCGACGTAGGTCTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2513:26:17,9:1445,1041:2486,26:0.0103:2,2:35.6:1:35:1:0.55086:1.36:60:52:0.0105:0.0016:0.1 0/0:2554:22:15,7:1486,1044:2530,22:0.0086:2,2:34.7:1:34.5:1:0.51482:1.51:60:44:0.0088:0.002:0.3
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chr12 133250118 133250118 C T intron POLE NM_006231:exon13:c.1359+43G>A . . rs4883555 ID=COSV57686697;OCCURENCE=1(liver) 1238209 Facial_dysmorphism,_immunodeficiency,_livedo,_and_short_stature|Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency|not_provided MONDO:MONDO:0014058,MedGen:C3554576,OMIM:615139,Orphanet:ORPHA352712|MONDO:MONDO:0032684,MedGen:C5193036,OMIM:618336|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.576478 0.6736 0.4926 0.5003 0.6234 0.5788 0.7124 0.4392 0.4275 0.4841 0.5444 0.5054 0.6283 0.5849 0.3833 0.7039 0.4326 0.4303 0.4651 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12q24.33 1 379 1926 chr12 133250118 . C T 379 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1878;VD=1863;AF=0.992;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32578;SOR=0.77874;LSEQ=GCTCCGTGGCCATCTGGATG;RSEQ=GTGCACACGGCAGCAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1878:1863:1240,623:1,1:2,1863:0.992:2,2:39.8:1:34.8:1:1:1.99:60:464.75:0.9931:0.0229:1.2 1/1:1926:1914:1288,626:1,0:1,1914:0.9938:0,2:38.7:1:34.8:1:1:0:60:272.429:0.9943:0.041:1.2
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chr12 133257837 133257837 C A exonic POLE . nonsynonymous SNV POLE:NM_006231:exon2:c.91G>T:p.A31S rs34047482 . 222245 Carcinoma_of_colon|Colorectal_cancer,_susceptibility_to,_12|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0014038,MedGen:C3554460,OMIM:615083|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.00878594 . 0.0160 0.0114 0.0031 0.0077 0.0001 0.0082 0.0163 0.0130 0.0093 0.0124 0.0045 0.0060 0 0 0.0072 0.0201 0.0153 0.439 0.093 T 0.000 0.491 D 1.000 0.588 D 1.385 0.346 L 4.22 0.031 T -0.16 0.095 N -0.911 0.468 T 0.004 0.013 T . . . . . 0.991 0.912 D c -0.298 -0.233 1.000 0.747 0.737 0.974 0 4.83 0.617 7.412 0.791 0.890 0.394 1.000 0.715 0.102 0.190 17.888 0.887 . . . 12q24.33 0.5 339 1995 chr12 133257837 . C A 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1917;VD=882;AF=0.4601;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0276;SOR=0.88264;LSEQ=CCGTTCCAGGCGCTTGAGTG;RSEQ=CGAAACTGAGGAAGTGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1917:882:442,440:510,519:1029,882:0.4601:2,2:39.5:1:34.5:1:0.81865:1.02:60:146:0.4662:0.0177:1.1 0/1:1995:980:454,526:480,530:1010,980:0.4912:2,2:37.9:1:34.2:1:0.62121:1.04923:60:80.667:0.4954:0.0231:1.1
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chr13 28592546 28592546 T C intronic FLT3 . . . rs17086226 ID=COSV54044799;OCCURENCE=1(bone),1(haematopoietic_and_lymphoid_tissue),1(liver),2(lung) 1235463 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.249002 0.251 . 0.2427 0.1522 0.2504 0.2467 0.1840 0.2147 0.2630 0.4041 0.1994 0.1467 0.2285 0.1987 0.2404 0.1786 0.2257 0.2480 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 344 1945 chr13 28592546 . T C 344 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1908;VD=975;AF=0.511;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41056;SOR=0.98348;LSEQ=GTGAGTGCAGTTGTTTACCA;RSEQ=GATAACGACACAACACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1908:975:723,252:655,274:929,975:0.511:2,2:37.6:1:34.4:1:0.0813:1.20:60:120.875:0.5098:0.022:1.1 1/0:1945:1002:726,276:695,245:940,1002:0.5152:2,2:37.3:1:34.6:1:0.47339:1.07837:60:199.4:0.5144:0.0237:1.1
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chr13 28597448 28597449 TC - splicing FLT3 NM_004119:exon19:r.spl . . rs35829721 ID=COSV99607994;OCCURENCE=2(central_nervous_system) 1276807 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.101637 0.0317 0.1600 0.1633 0.0661 0.1275 0.0238 0.2405 0.2070 0.1535 0.1309 0.1515 0.0624 0.1423 0.23 0.0228 0.2266 0.1964 0.1837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 327 1299 chr13 28597447 . ATC A 327 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1331;VD=618;AF=0.4643;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02678;SOR=0.85752;LSEQ=ATATAAGCACATCTTTTCAA;RSEQ=TTTTTTTTGGTTTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1331:618:427,191:464,238:702,618:0.4643:2,2:38.7:1:34.9:1:0.26329:1.15:60:1236:0.4668:0.0661:0.1 1/0:1299:653:454,199:405,234:639,653:0.5027:2,2:39.9:1:35:1:0.02149:1.32:60:1306:0.5031:0.0824:0.1
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chr13 28609813 28609813 - A intron FLT3 NM_004119:exon12:c.1419-3->T . . rs574116870 . . . . . . 0.00559105 . . 0.0069 0.0041 0.0026 0.0042 0.0006 0.0032 0.0086 0.0335 0.0007 0.0011 0.0013 0 0.0006 0.0004 0.0001 0.0057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 231 1718 chr13 28609813 . G GA 231 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1684;VD=79;AF=0.0469;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.07056;SOR=0.78808;LSEQ=GTGATCTCTTCTGTGCAGCT;RSEQ=AAAAAAAAAATAGCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1684:79:31,47:627,784:1411,79:0.0469:2,2:47.7:1:34.9:1:0.48254:1.21236:60:158:0.0569:0:0.9 0/1:1718:101:38,63:647,779:1426,101:0.0588:2,2:44.6:1:34.8:1:0.14731:1.37668:60:202:0.0713:0.0029:1.2
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chr13 28609825 28609825 A G intron FLT3 NM_004119:exon12:c.1419-15T>C . . rs2491227 ID=COSV54057797;OCCURENCE=10(meninges),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),1(upper_aerodigestive_tract) 1275848 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.563099 0.7351 0.6164 0.6990 0.2735 0.7199 0.7454 0.7993 0.7724 0.7070 0.6105 0.6230 0.2617 0.7110 0.7450 0.7574 0.8025 0.7641 0.7172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 325 1541 chr13 28609825 . A G 325 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1528;VD=711;AF=0.4653;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42928;SOR=0.98461;LSEQ=GTGCAGCTGAAAAAAAAAAT;RSEQ=GCAAAGAATTTAGACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1528:711:294,417:360,456:816,711:0.4653:2,2:41.6:1:33.8:1:0.27694:1.11968:60:43.438:0.4609:0.0203:1.9 0/1:1541:723:283,440:372,444:816,723:0.4692:2,2:42.9:1:34.3:1:0.01139:1.30241:60:89.375:0.4667:0.0149:1.9
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chr13 28610183 28610183 A G intron FLT3 NM_004119:exon11:c.1310-3T>C . . rs2491231 ID=COSV54043781;OCCURENCE=1(breast),17(meninges),2(central_nervous_system),1(bone),2(haematopoietic_and_lymphoid_tissue),1(soft_tissue) 1281808 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.563299 0.7351 0.6164 0.6965 0.2730 0.7191 0.7460 0.7989 0.7715 0.7032 0.6010 0.6236 0.261 0.7117 0.7450 0.7584 0.8029 0.7639 0.7198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 328 1433 chr13 28610183 . A G 328 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1438;VD=709;AF=0.493;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28152;SOR=0.95506;LSEQ=CGAGCACTTGAGGTTTCCCT;RSEQ=TAGAAAAGAACGTGTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1438:709:328,381:330,397:727,709:0.493:2,2:42.4:1:34.7:1:0.75084:1.04:60:708:0.4941:0.0139:1.1 1/0:1433:723:315,408:331,376:707,723:0.5045:2,2:41.6:1:34.6:1:0.222:1.14012:60:119.5:0.5039:0.0195:1.1
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chr13 28611382 28611382 T G exonic FLT3 . nonsynonymous SNV FLT3:NM_004119:exon10:c.1249A>C:p.I417L rs56090538 ID=COSV99058810;OCCURENCE=3(lung) 138172 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0109824 . 0.0111 0.0033 0.0345 0.0015 0 0 0.0004 0 0 0.0092 0.0316 0.0036 0 0 0 0.0001 0.0041 0.09 0.319 T 0.013 0.289 N 1.000 0.198 N 1.5 0.380 L -0.99 0.759 T -0.24 0.108 N -0.985 0.339 T 0.094 0.357 T . . . . . 0.155 0.187 N c -0.547 -0.397 1.000 0.458 0.560 0.301 0 3.63 0.406 0.123 0.154 1.061 0.807 0.132 0.232 1.000 0.888 6.669 0.221 Immunoglobulin-like fold . . 13q12.2 0.5 328 1435 chr13 28611382 . T G 328 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1445;VD=729;AF=0.5045;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.36752;SOR=0.97238;LSEQ=ATCATTTTCTGCATGGAATA;RSEQ=ATATTCTCCTGGCTGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1445:729:446,283:410,306:716,729:0.5045:2,2:41:1:34.4:1:0.1341:1.18:60:103.143:0.5024:0.0062:1.1 1/0:1435:734:387,347:423,276:699,734:0.5115:2,2:41.9:1:34.5:1:0.00336:1.37387:60:182.5:0.5108:0.0063:1.1
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chr13 28623699 28623699 G T intron FLT3 NM_004119:exon8:c.883-25C>A . . rs9507985 ID=COSV54055198;OCCURENCE=9(meninges),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),1(upper_aerodigestive_tract) 1251760 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.107827 0.0496 0.1623 0.1660 0.0678 0.1286 0.0413 0.2423 0.2092 0.1556 0.1321 0.1551 0.0659 0.1432 0.2318 0.0444 0.2279 0.1992 0.1857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 354 2437 chr13 28623699 . G T 354 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2349;VD=1132;AF=0.4819;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47295;SOR=1.00562;LSEQ=GTTTTAATAAAACAGAGTTT;RSEQ=CATTTAATGTTTTCAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2349:1132:621,511:636,577:1213,1132:0.4819:2,2:36.4:1:34.9:1:0.24613:1.10:60:376.333:0.4841:0.0238:1.7 0/1:2437:1171:634,537:687,576:1263,1171:0.4805:2,2:35.7:1:34.8:1:0.90285:1.01023:60:584.5:0.4825:0.0263:1.7
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chr13 28623759 28623759 C T intron FLT3 NM_004119:exon7:c.882+13G>A . . rs9513004 ID=COSV54055206;OCCURENCE=9(meninges),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 1243361 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.102436 0.0496 0.1553 0.1589 0.0667 0.1250 0.0407 0.2384 0.1978 0.1527 0.1288 0.1485 0.0639 0.1364 0.2285 0.0438 0.2230 0.1888 0.1776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 353 2321 chr13 28623759 . C T 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2262;VD=1090;AF=0.4819;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4143;SOR=1.01466;LSEQ=CTGCATTTTCAGAATACAAA;RSEQ=TTGTCCTATTACCTCCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2262:1090:589,501:615,555:1170,1090:0.4819:2,2:38:1:34.8:1:0.49974:1.06:60:1089:0.4851:0.0168:1.6 0/1:2321:1110:604,506:627,583:1210,1110:0.4782:2,2:37.3:1:34.9:1:0.21194:1.11:60:554:0.4803:0.0168:1.6
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chr13 28623938 28623938 - A intron FLT3 NM_004119:exon7:c.743-27->T . . rs67491524 ID=COSV99608007;OCCURENCE=2(central_nervous_system) 1261201 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.106629 0.0486 0.1619 0.1675 0.0696 0.1300 0.0427 0.2409 0.2096 0.1534 0.1377 0.1612 0.0677 0.1460 0.2365 0.0448 0.2505 0.2065 0.1978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.5 328 1490 chr13 28623938 . G GA 328 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1571;VD=684;AF=0.4354;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.06756;SOR=1.11862;LSEQ=GATGAAAACATCCCAAGTGA;RSEQ=AAAAAAAAAGTGATTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1571:684:277,407:302,413:715,684:0.4354:2,2:45.2:1:34.9:1:0.51513:1.07436:60:1368:0.9785:0.0121:0.1 0/1:1490:608:240,368:318,420:738,608:0.4081:2,2:46:1:34.9:1:0.18269:1.16082:60:607:0.8407:0:0.1
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chr13 28636084 28636084 G A exonic FLT3 . synonymous SNV FLT3:NM_004119:exon3:c.288C>T:p.D96D rs7338903 ID=COSV54043799;OCCURENCE=18(meninges),2(central_nervous_system) 1270029 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.958067 0.996 0.9599 0.9831 0.8963 0.9909 0.9987 0.9961 0.9882 0.9971 0.9956 0.9662 0.9027 0.9869 0.9967 0.9994 0.9957 0.9893 0.9898 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 1 385 2193 chr13 28636084 . G A 385 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2153;VD=2138;AF=0.993;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0.9158;LSEQ=CAGGAAATGTTCCCTGGGGC;RSEQ=TCGACCAGCACTTGCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2153:2138:1223,915:0,1:1,2138:0.993:0,2:39.3:1:34.8:1:0.42824:0:60:426.6:0.9967:0.0093:1.1 1/1:2193:2179:1294,885:2,1:3,2179:0.9936:2,2:38.3:1:34.8:1:1:1.36766:60:271.375:0.9977:0.0369:1.1
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chr13 28674581 28674584 GCGA - splicing FLT3 NM_004119:exon1:r.spl . . . . . . . . . . . . . . . . . . . . 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q12.2 0.25 140 1473 chr13 28674580 . TGCGA T 140 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=1719;VD=13;AF=0.0076;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.21381;SOR=0.694;LSEQ=GCTGAGGGACCGCGAGGGGC;RSEQ=GCGAGCGAGCGGGGCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1719:13:6,7:1069,635:1704,13:0.0076:2,2:48.8:1:35:0:0.25444:1.96328:60:26:0.0076:0:0.5 0/1:1473:16:11,5:918,538:1456,16:0.0109:2,2:47.1:1:35:1:0.79661:1.29:60:32:0.011:0.0014:0.6
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chr13 28674628 28674628 T C exonic FLT3 . nonsynonymous SNV FLT3:NM_004119:exon1:c.20A>G:p.D7G rs12872889 ID=COSV54062407;OCCURENCE=7(meninges),1(thyroid) 1240691 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.373602 0.3304 . 0 . . . . . . . 0.3645 0.6005 0.1619 0.1747 0.3531 0.2879 0.2633 0.3096 0.797 0.031 T 0.866 0.071 N 1.000 0.090 P 0 0.065 N -1.07 0.770 T 0.4 0.035 N -0.943 0.422 T 0.000 0.000 T . . . . . 0.004 0.019 N c -1.120 -1.022 1.000 0.747 0.564 0.319 0 2.1 0.261 -1.692 0.020 -0.043 0.124 0.000 0.063 0.961 0.442 4.099 0.094 . ENSG00000261485.1 Colon_Transverse 13q12.2 0.5 336 1653 chr13 28674628 . T C 336 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1921;VD=921;AF=0.4794;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35158;SOR=0.97254;LSEQ=GCAGCGGCAGCTGGCCGCCG;RSEQ=CGCGCGCCAACGCCGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1921:921:477,444:540,451:991,921:0.4794:2,2:39.7:1:34.2:1:0.25158:1.11444:60:91.1:0.489:0.0115:1.2 0/1:1653:804:428,376:469,375:844,804:0.4864:2,2:39.9:1:34.1:1:0.34755:1.09865:60:79.4:0.4978:0.0109:1.2
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chr13 32890572 32890572 G A intron BRCA2 NM_000059:c.-26G>A . . rs1799943 ID=COSV61525225;OCCURENCE=9(meninges),2(central_nervous_system),1(bone),1(haematopoietic_and_lymphoid_tissue),2(upper_aerodigestive_tract) 131503 Hereditary_breast_and_ovarian_cancer_syndrome|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.209265 0.3601 0.2088 0.2448 0.0994 0.1885 0.3838 0.1922 0.2552 0.2653 0.2831 0.2208 0.1112 0.1842 0.2815 0.3857 0.1990 0.2722 0.2301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 320 1084 chr13 32890572 . G A 320 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1168;VD=595;AF=0.5094;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20492;SOR=0.9295;LSEQ=TTTGCAGACTTATTTACCAA;RSEQ=CATTGGAGGAATATCGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1168:595:399,196:381,188:569,595:0.5094:2,2:39.7:1:34.8:1:1:1.00:60:594:0.5143:0.0146:1.1 1/0:1084:572:372,200:325,187:512,572:0.5277:2,2:41.5:1:34.9:1:0.61176:1.07:60:571:0.5292:0.0166:1.1
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chr13 32893197 32893197 - T intron BRCA2 NM_000059:exon3:c.68-17->T . . rs397507376 . 46621 Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . 0.0042 0.0006 0.0015 0.0002 0.0001 0 0.0004 0.0016 0.0013 0.0004 0.0012 0 0 0 0 0.0001 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 207 1653 chr13 32893197 . A AT 207 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1685;VD=63;AF=0.0374;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.52901;SOR=0.99671;LSEQ=CTGGTTAAAACTAAGGTGGG;RSEQ=TTTTTTTTTTAAATAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1685:63:37,26:892,542:1434,63:0.0374:2,2:35.7:1:34.7:1:0.59712:1.15636:60:126:0.0441:0.0047:0.1 0/1:1653:62:41,21:840,566:1406,62:0.0375:2,2:37.6:1:34.6:1:0.3551:1.32:60:124:0.0443:0.003:0.1
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chr13 32907421 32907421 A - exonic BRCA2 . frameshift deletion BRCA2:NM_000059:exon10:c.1806delA:p.I605Yfs*9 rs80359307 ID=COSV66449038;OCCURENCE=5(large_intestine),1(biliary_tract),2(ovary),1(stomach),2(haematopoietic_and_lymphoid_tissue) 46319 Hereditary_breast_and_ovarian_cancer_syndrome|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202 reviewed_by_expert_panel Pathogenic . . 0.0120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.25 153 1686 chr13 32907420 . GA G 153 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=1782;VD=11;AF=0.0062;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.039;SOR=0.49256;LSEQ=TGATGAAACATCTTATAAAG;RSEQ=AAAAAAATACCGAAAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1782:11:7,4:1061,710:1771,11:0.0062:2,2:42.7:1:35:0:1:1.17:60:22:0.0062:0:0 0/1:1686:21:14,7:981,684:1665,21:0.0125:2,2:32.5:1:35:1:0.51294:1.39:60:42:0.0125:0.0018:0
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chr13 32907536 32907536 T - intron BRCA2 NM_000059:exon10:c.1909+12T>- . . rs276174816 ID=COSV66463516;OCCURENCE=1(liver),1(large_intestine) 136530 Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity . . 0.0814 0.1777 0.1465 0.1954 0.1592 0.0664 0.1787 0.1644 0.2355 0.0026 0.0005 0.0070 0.0039 0 0.0214 0.0010 0.0076 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 252 1333 chr13 32907535 . CT C 252 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1385;VD=147;AF=0.1061;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.31827;SOR=0.93651;LSEQ=GCTGATTCAGGTACCTCTGT;RSEQ=TTTTTTTTTTGTAAATAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1385:147:67,80:541,674:1215,147:0.1061:2,2:42.7:1:35:1:0.86063:1.04:60:294:0.1063:0.0051:0.1 0/1:1333:150:59,91:525,632:1157,150:0.1125:2,2:43:1:34.9:1:0.16395:1.281:60:300:0.1125:0.0098:0.2
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chr13 32911888 32911888 A G exonic BRCA2 . synonymous SNV BRCA2:NM_000059:exon11:c.3396A>G:p.K1132K rs1801406 ID=COSV66448451;OCCURENCE=1(breast),10(meninges),2(central_nervous_system),1(bone),1(haematopoietic_and_lymphoid_tissue),1(urinary_tract),2(lung) 131548 Hereditary_breast_and_ovarian_cancer_syndrome|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.266773 0.3681 0.2798 0.2927 0.2309 0.2070 0.3876 0.3090 0.3044 0.3188 0.2925 0.2984 0.2348 0.2100 0.3212 0.3863 0.3113 0.3267 0.3108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 352 2412 chr13 32911888 . A G 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2310;VD=1130;AF=0.4892;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02801;SOR=0.89319;LSEQ=GAATTTACTCAGTTTAGAAA;RSEQ=CCAAGCTACATATTGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2310:1130:677,453:697,481:1178,1130:0.4892:2,2:37.5:1:34.2:1:0.73441:1.03:60:58.474:0.486:0.0177:1.1 1/0:2412:1248:782,466:686,476:1162,1248:0.5174:2,2:36.9:1:34.3:1:0.07247:1.16:60:77:0.5159:0.0166:1.1
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chr13 32913055 32913055 A G exonic BRCA2 . synonymous SNV BRCA2:NM_000059:exon11:c.4563A>G:p.L1521L rs206075 ID=COSV101203861;OCCURENCE=18(meninges),2(central_nervous_system) 136527 Hereditary_breast_and_ovarian_cancer_syndrome|Malignant_tumor_of_breast|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.974042 1 0.9758 0.9930 0.9250 0.9968 1 1 0.9995 0.9986 0.9999 0.9799 0.9301 0.9976 1 0.9994 1 0.9997 0.9959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 1 371 1743 chr13 32913055 . A G 371 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1723;VD=1718;AF=0.9971;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29747;SOR=1.58411;LSEQ=AAGATCAAAGAACCTACTCT;RSEQ=TTGGGTTTTCATACAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1723:1718:1005,713:1,1:2,1718:0.9971:2,2:35.8:1:34.3:1:1:1.41:60:77.091:0.9976:0.0546:1.1 1/1:1743:1735:1027,708:1,0:1,1735:0.9954:0,2:36.1:1:34.5:1:1:0:60:172.5:0.9965:0.0413:1.1
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chr13 32915005 32915005 G C exonic BRCA2 . synonymous SNV BRCA2:NM_000059:exon11:c.6513G>C:p.V2171V rs206076 ID=COSV66458663;OCCURENCE=1(thyroid),18(meninges),2(central_nervous_system) 136528 Hereditary_breast_and_ovarian_cancer_syndrome|Malignant_tumor_of_breast|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.973642 1 0.9755 0.9929 0.9237 0.9968 1 1 0.9995 0.9986 0.9998 0.9798 0.9299 0.9976 1 0.9994 1 0.9997 0.9959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 1 375 1827 chr13 32915005 . G C 375 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1963;VD=1956;AF=0.9964;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.55256;SOR=0.92074;LSEQ=TTGGTATTAGGAACCAAAGT;RSEQ=TCACTTGTTGAGAACATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1963:1956:1079,877:0,0:0,1956:0.9964:0,2:36.6:1:34.3:1:1:0:60:66.448:0.9979:0.0418:1.1 1/1:1827:1821:993,828:0,0:0,1821:0.9967:0,2:37.9:1:34.3:1:1:0:60:64.036:0.9972:0.023:1.1
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chr13 32918304 32918305 AA - intronic BRCA2 . . . rs57432465 . . . . . . . . . . . . . . . . . 0.2238 0.2749 0.2150 0.1614 0.0968 0.2761 0.2075 0.2136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 287 944 chr13 32918303 . GAA G 287 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1067;VD=316;AF=0.2962;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=0.5105;SOR=0.99783;LSEQ=TTAATGGCTGCCCCCGTGCT;RSEQ=AAAAAAAAAAAAAAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1067:316:194,122:322,174:496,316:0.2962:2,2:41.1:1:34.6:1:0.33118:1.16354:60:315:0.2958:0.0206:0.1 0/1:944:280:167,113:228,162:390,280:0.2966:2,2:44:1:34.9:1:0.81127:1.05:60:560:0.2985:0.0064:0.2
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chr13 32929232 32929232 A G exonic BRCA2 . synonymous SNV BRCA2:NM_000059:exon14:c.7242A>G:p.S2414S rs1799955 ID=COSV66447569;OCCURENCE=1(breast),6(meninges),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),11(soft_tissue) 131671 Hereditary_breast_and_ovarian_cancer_syndrome|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.232628 0.369 0.2114 0.2245 0.2135 0.1782 0.3874 0.2362 0.2132 0.2305 0.2164 0.2299 0.2206 0.1627 0.2219 0.3837 0.2261 0.2239 0.2255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 338 2091 chr13 32929232 . A G 338 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2038;VD=957;AF=0.4696;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26816;SOR=0.9603;LSEQ=CCACCTTTTAAAACTAAATC;RSEQ=CATTTTCACAGAGTTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2038:957:593,364:623,456:1079,957:0.4696:2,2:37.9:1:33.8:1:0.05724:1.19:60:49.368:0.4655:0.0088:1.1 0/1:2091:1003:588,415:645,439:1084,1003:0.4797:2,2:37.5:1:34:1:0.68866:1.03697:60:54.722:0.4756:0.0201:1.1
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chr13 32929387 32929387 T C exonic BRCA2 . nonsynonymous SNV BRCA2:NM_000059:exon14:c.7397T>C:p.V2466A rs169547 ID=COSV66451785;OCCURENCE=1(peritoneum),18(meninges),2(central_nervous_system) 137477 Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_2|Ductal_breast_carcinoma|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MedGen:C1527349|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.975839 1 0.9777 0.9936 0.9315 0.9970 1 1 0.9996 0.9986 0.9998 0.9819 0.9369 0.9976 1 0.9994 1 0.9997 0.9980 1.0 0.010 T 0.194 0.168 N 1 0.090 P . . . 5.95 0.007 T 0.62 0.024 N -0.930 0.442 T 0.000 0.000 T . . . . . 0.000 0.004 N c -0.614 -0.667 1.000 0.436 0.651 0.465 0 5.07 0.680 2.491 0.447 -0.023 0.128 0.028 0.201 0.005 0.090 12.092 0.528 . . . 13q13.1 1 368 1779 chr13 32929387 . T C 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1797;VD=1792;AF=0.9972;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02992;SOR=2.84218;LSEQ=AAACAACTCCAATCAAGCAG;RSEQ=AGCTGTAACTTTCACAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1797:1792:973,819:0,0:0,1792:0.9972:0,2:37.6:1:34.1:1:1:0:60:56.806:0.9989:0.0351:1.1 1/1:1779:1765:990,775:1,2:3,1765:0.9921:2,2:37.8:1:34:1:0.58548:2.55:60:42.049:0.9954:0.027:1.1
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chr13 32936646 32936646 T C intron BRCA2 NM_000059:exon17:c.7806-14T>C . . rs9534262 ID=COSV66447577;OCCURENCE=1(liver),13(meninges),2(central_nervous_system),20(soft_tissue),1(lung) 131696 Hereditary_breast_and_ovarian_cancer_syndrome|Fanconi_anemia,_complementation_group_D1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|Breast_and/or_ovarian_cancer|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011584,MedGen:C1838457,OMIM:605724,Orphanet:ORPHA319462|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN221562|MedGen:CN517202 reviewed_by_expert_panel Benign 0.53155 0.5337 0.5202 0.5208 0.5725 0.5085 0.5568 0.5760 0.5132 0.4971 0.4882 0.5470 0.5768 0.5167 0.4633 0.5527 0.5659 0.5281 0.5468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 1 353 1319 chr13 32936646 . T C 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1329;VD=1328;AF=0.9992;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10735;SOR=5.0505;LSEQ=TTTTTATGATAATATTCTAC;RSEQ=TTTATTTGTTCAGGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1329:1328:902,426:0,0:0,1328:0.9992:0,2:42.7:1:34.1:1:1:0:60:59.364:1:0:1.1 1/1:1319:1314:905,409:1,0:1,1314:0.9962:0,2:41.2:1:34.3:1:1:0:60:68.158:1:0.0387:1.1
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chr13 32954022 32954022 - A exonic BRCA2 . frameshift insertion BRCA2:NM_000059:exon23:c.9090dupA:p.T3033Nfs*11 rs397507419 ID=COSV66447774;OCCURENCE=1(breast),1(large_intestine),2(stomach),1(haematopoietic_and_lymphoid_tissue),1(prostate),1(lung),9(upper_aerodigestive_tract) 46764 Breast_carcinoma|Neoplasm_of_ovary|Hereditary_breast_and_ovarian_cancer_syndrome|Malignant_tumor_of_breast|Breast-ovarian_cancer,_familial_1|Breast-ovarian_cancer,_familial_2|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|Breast_and/or_ovarian_cancer|not_provided Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0012933,MedGen:C2675520,OMIM:612555|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN221562|MedGen:CN517202 reviewed_by_expert_panel Pathogenic . . . 9.003e-05 0 9.407e-05 0 0 0.0002 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.5 162 1910 chr13 32954022 . C CA 162 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1995;VD=23;AF=0.0115;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.38304;SOR=0.87944;LSEQ=TAACATACAGTTAGCAGCGA;RSEQ=AAAAAAAACTCAGTATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1995:23:12,10:1138,738:1876,23:0.0115:2,2:35.2:1:34.9:1:0.66173:1.28481:60:46:0.0124:0.0015:0.2 0/1:1910:25:15,9:1046,668:1714,25:0.0131:2,2:41.2:1:35:1:1:1.06:60:50:0.0147:0.001:0.2
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chr13 32954302 32954302 - T intron BRCA2 NM_000059:exon24:c.9256+20->T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q13.1 0.25 121 987 chr13 32954302 . A AT 121 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Insertion;DP=1014;VD=9;AF=0.0089;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.38775;SOR=0.79467;LSEQ=GGTAATGCACAATATAGTTA;RSEQ=TTTTTTTTATTGATTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1014:9:3,6:377,581:958,9:0.0089:2,2:36.9:1:35:0:1:1.29742:60:18:0.0095:0:0 0/1:987:11:5,6:371,559:930,11:0.0111:2,2:39:1:35:1:0.76207:1.26:60:22:0.0119:0.002:0.3
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chr13 48881570 48881570 - T intron RB1 NM_000321:exon2:c.264+28->T . . rs766242952 ID=COSV99924869;OCCURENCE=1(stomach) . . . . . . . . 5.765e-05 0 9.029e-05 0 0.0002 7.51e-05 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 0.25 153 1095 chr13 48881570 . A AT 153 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Insertion;DP=1023;VD=9;AF=0.0088;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03191;SOR=0.45412;LSEQ=TTTTCTTAAAACGTTTTGAA;RSEQ=TTTTTTTTTCTCATTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1023:9:3,6:426,534:960,9:0.0088:2,2:47.2:1:35:0:0.73861:1.59477:60:18:0.0094:0:0 0/1:1095:21:11,9:423,539:962,21:0.0192:2,2:48.6:1:35:0:0.36758:1.56:60:42:0.0219:0:0.1
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chr13 48922032 48922032 A - intron RB1 NM_000321:exon5:c.539+33A>- . . rs749607535 ID=COSV57297267;OCCURENCE=2(large_intestine),1(stomach),1(prostate) . . . . . . . . 0.0015 0.0015 0.0024 0.0019 0 0.0015 0.0019 0.0011 3.306e-05 0 0 0 0 0 6.793e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 0.5 156 669 chr13 48922031 . TA T 156 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=718;VD=21;AF=0.0292;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.40644;SOR=0.88615;LSEQ=ACAGAATGTTATTTTTCACT;RSEQ=AAAAAAAAGATTTTTATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:21:10,11:342,352:694,21:0.0292:2,2:38.8:1:35:0:1:1.06868:60:42:0.0294:0:0.2 0/1:669:22:12,10:326,317:643,22:0.0329:2,2:51.8:1:35:0:0.82949:1.17:60:44:0.0329:0:0
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chr13 48954160 48954160 T - intron RB1 NM_000321:exon15:c.1390-29T>- . . rs755845243 ID=COSV57297827;OCCURENCE=1(meninges),4(biliary_tract),1(bone) 487696 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . 0.0613 0.4171 0.2483 0.3636 0.3679 0.0756 0.3995 0.4286 0.4544 0.0040 0.0009 0.0217 0.0231 0 0.0222 0.0047 0.0050 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 0.5 201 315 chr13 48954159 . CT C 201 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=294;VD=49;AF=0.1667;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.28798;SOR=0.868;LSEQ=AGGTTTCAATTAAACAACTT;RSEQ=TTTTTTTTTTTTAAATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:49:38,11:147,78:225,49:0.1667:2,2:38:1:34.8:1:0.12917:1.83:60:98:0.1678:0.0102:0.1 0/1:315:59:37,22:166,71:237,59:0.1873:2,2:42.6:1:34.2:1:0.27747:1.38862:60:118:0.1873:0.019:0.2
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chr13 48954283 48954283 T - intron RB1 NM_000321:exon16:c.1422-18T>- . . rs750651121 ID=COSV57299963;OCCURENCE=1(large_intestine) 266127 not_specified MedGen:CN169374 criteria_provided,_single_submitter Benign . . 0.1601 0.3224 0.3134 0.3760 0.3722 0.2240 0.3448 0.3214 0.3017 0.0026 0.0010 0.0017 0.0039 0.0099 0.0110 0.0018 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 0.5 232 885 chr13 48954282 . CT C 232 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=941;VD=102;AF=0.1084;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.43941;SOR=1.03532;LSEQ=AGAAGTAAGTATTTTATAAT;RSEQ=TTTTTTTTTTCCTTTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:941:102:68,34:554,270:824,102:0.1084:2,2:37.3:1:34.8:1:0.91132:1.02592:60:101:0.1079:0.0149:0.2 0/1:885:93:62,31:535,242:777,93:0.1051:2,2:40.7:1:35:1:0.72291:1.10524:60:186:0.1051:0.0068:0.1
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chr13 48955364 48955364 T - intron RB1 NM_000321:exon17:c.1499-19T>- . . rs148580581 ID=COSV57296314;OCCURENCE=2(large_intestine),2(biliary_tract) 621833 Malignant_tumor_of_urinary_bladder|not_specified MONDO:MONDO:0001187,MedGen:C0005684,OMIM:109800,Orphanet:ORPHA157980,SNOMED_CT:399326009|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . 0.0708 0.0408 0.0341 0.0656 0.0490 0.0261 0.0486 0.0327 0.0283 0.0008 0.0009 0.0013 0.0036 0.0006 0 0.0008 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 0.5 202 1341 chr13 48955363 . CT C 202 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1301;VD=58;AF=0.0446;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32507;SOR=1.11205;LSEQ=TAATATTTCATAAATAGTTA;RSEQ=TTTTTTTTTCATTTTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1301:58:42,16:831,407:1238,58:0.0446:2,2:43.8:1:34.6:1:0.47452:1.29:60:116:0.0447:0.0031:0.1 0/1:1341:54:42,12:863,417:1280,54:0.0403:2,2:43.6:1:35:1:0.13642:1.69:60:108:0.0404:0.0022:0.1
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chr13 49051012 49051012 C T intron RB1 NM_000321:exon25:c.2663+33C>T . . rs3020646 ID=COSV99922909;OCCURENCE=18(meninges),2(central_nervous_system) 254858 Retinoblastoma|not_specified|not_provided Human_Phenotype_Ontology:HP:0009919,MONDO:MONDO:0008380,MeSH:D012175,MedGen:C0035335,OMIM:180200,Orphanet:ORPHA790|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.884984 0.998 0.8958 0.9549 0.7191 0.9501 0.9978 0.9986 0.9824 0.9625 0.9584 0.9146 0.7288 0.9415 0.9404 0.9957 0.9991 0.9877 0.9817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 1 368 1556 chr13 49051012 . C T 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1536;VD=1529;AF=0.9954;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03359;SOR=0.14054;LSEQ=TTTGAATGTTTTCCAGTAGC;RSEQ=GAGATGGTCATCTGGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1536:1529:715,814:2,2:4,1529:0.9954:2,2:43.3:1:34.8:1:1:1.13836:60:381.25:0.9967:0.0267:1.1 1/1:1556:1555:737,818:0,0:0,1555:0.9994:0,2:42.4:1:34.8:1:1:0:60:193.375:0.9994:0.0257:1.1
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chr13 49051481 49051481 T A intron RB1 NM_000321:exon26:c.2664-10T>A . . rs3092904 ID=COSV57294376;OCCURENCE=1(breast),6(meninges),1(stomach),9(soft_tissue) 98750 Retinoblastoma|not_specified|not_provided Human_Phenotype_Ontology:HP:0009919,MONDO:MONDO:0008380,MeSH:D012175,MedGen:C0035335,OMIM:180200,Orphanet:ORPHA790|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.188698 0.2371 0.1955 0.2615 0.1028 0.2190 0.2518 0.2800 0.2859 0.2540 0.2941 0.2142 0.0939 0.2129 0.1933 0.2354 0.2806 0.2628 0.2791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13q14.2 0.5 317 1126 chr13 49051481 . T A 317 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1105;VD=544;AF=0.4923;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49449;SOR=1.00477;LSEQ=TGAAATGTTTTGCATTTTTT;RSEQ=AATCTGCAGTAAACATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1105:544:383,161:378,182:560,544:0.4923:2,2:38.7:1:34.6:1:0.299:1.15:60:180.333:0.4918:0.0136:1.1 0/1:1126:553:381,172:389,184:573,553:0.4911:2,2:38.8:1:34.8:1:0.74866:1.05:60:275.5:0.4907:0.0124:1.1
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chr14 45606387 45606387 A G exonic FANCM . nonsynonymous SNV FANCM:NM_001308133:exon2:c.624A>G:p.I208M,FANCM:NM_001308134:exon2:c.624A>G:p.I208M,FANCM:NM_020937:exon2:c.624A>G:p.I208M rs45547534 ID=COSV53531926;OCCURENCE=1(large_intestine),1(soft_tissue) 241831 Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.00539137 . 0.0114 0.0102 0.0028 0.0057 0 0.0050 0.0145 0.0087 0.0101 0.0081 0.0021 0.0107 0.0033 0 0.0049 0.0132 0.0071 0.007 0.682 D 0.000 0.497 N 0.845 0.285 N 3.225 0.897 M 2.38 0.158 T -2.48 0.540 N -1.072 0.090 T 0.032 0.138 T . . . . . 0.701 0.342 D c 0.299 0.189 0.999 0.393 0.609 0.349 0 0.008 0.133 0.019 0.132 1.199 0.960 0.836 0.300 0.995 0.604 1.433 0.022 Helicase superfamily 1/2, ATP-binding domain|Helicase/UvrB, N-terminal|P-loop containing nucleoside triphosphate hydrolase . . 14q21.2 0.5 334 2101 chr14 45606387 . A G 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2171;VD=830;AF=0.3823;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23756;SOR=1.04825;LSEQ=GCTTGTCCCGCTGCTGAAAT;RSEQ=AAGTGTTTAGTTATTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2171:830:439,391:759,582:1341,830:0.3823:2,2:37.8:1:34.5:1:0.09181:1.16145:60:206.5:0.3812:0.0161:1.1 0/1:2101:780:389,391:716,605:1321,780:0.3713:2,2:37.9:1:34.6:1:0.05759:1.18945:60:129:0.3698:0.0148:1.1
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chr14 45609819 45609819 - T intron FANCM NM_020937:exon3:c.682-16->T;NM_001308134:exon3:c.682-16->T . . rs759364320 . . . . . . . . . 6.711e-05 0.0003 0 0 0 3.737e-05 0 0.0001 6.49e-05 0.0002 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q21.2 0.5 168 1344 chr14 45609819 . C CT 168 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1428;VD=28;AF=0.0196;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.53534;SOR=1.01384;LSEQ=GAACAGATGAAACTAAAGAA;RSEQ=TTTTTTTTTCTTAAGGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1428:28:15,12:947,380:1327,28:0.0196:2,2:43.3:1:35:1:0.08618:1.99263:60:56:0.0218:0.0021:0.1 0/1:1344:26:16,9:852,396:1248,26:0.0193:2,2:39.6:1:35:1:0.66716:1.21002:60:52:0.0211:0.0022:0.2
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chr14 45628284 45628285 TA - splicing FANCM NM_020937:exon9:r.spl;NM_001308133:exon8:r.spl;NM_001308134:exon9:r.spl . . rs112326758 . 254944 Spermatogenic_failure_28|Premature_ovarian_failure_15|not_specified|not_provided MONDO:MONDO:0054732,MedGen:C4748117,OMIM:618086|MONDO:MONDO:0054862,MedGen:C4748170,OMIM:618096|MedGen:CN169374|MedGen:CN517202 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity 0.118211 0.121 0.1649 0.3087 0.1507 0.3906 0.4057 0.2824 0.3209 0.3220 0.2884 0.0920 0.0395 0.1379 0.1336 0.1094 0.1215 0.1082 0.1366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q21.2 0.5 180 989 chr14 45628283 . TTA T 180 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1015;VD=36;AF=0.0355;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.05084;SOR=1.61592;LSEQ=AAAAGTTGTAATTAAAGTTT;RSEQ=TATATATATATAGCTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1015:36:22,14:614,363:977,36:0.0355:2,2:39.8:1:35:1:0.86152:1.0763:60:72:0.0355:0.0069:0.1 0/1:989:22:14,8:616,350:966,22:0.0222:2,2:41.4:1:34.5:1:1:1.00571:60:44:0.0223:0.003:0.1
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chr14 45639981 45639981 C - intron FANCM NM_020937:exon12:c.2160+32C>-;NM_001308133:exon11:c.2082+32C>- . . rs768447621 ID=COSV57499437;OCCURENCE=1(large_intestine),4(stomach) . . . . . . . . 5.731e-05 0 0 0 0 7.447e-05 0 0.0001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q21.2 0.5 133 1127 chr14 45639980 . TC T 133 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1161;VD=15;AF=0.0129;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.45629;SOR=1.12157;LSEQ=TATATTTTCAGATGTTCTTT;RSEQ=CCCCCCCTCATTTTAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1161:15:3,12:421,725:1146,15:0.0129:2,2:36.3:1:34.1:1:0.28:2.32131:60:30:0.0134:0.0017:0.1 0/1:1127:13:6,7:401,710:1111,13:0.0115:2,2:52.4:1:35:0:0.56313:1.52:60:26:0.012:0:0.1
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chr14 45642288 45642289 CT - exonic FANCM . stopgain FANCM:NM_001308133:exon12:c.2113_2114del:p.S708*,FANCM:NM_020937:exon13:c.2191_2192del:p.S734* rs772674591 ID=COSV57497426;OCCURENCE=2(NS),2(skin),1(large_intestine) . . . . . . . . 3.773e-05 0.0001 0 0 0 5.526e-05 0 0 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q21.2 0.25 160 2382 chr14 45642287 . ACT A 160 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2329;VD=26;AF=0.0112;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.35707;SOR=1.15789;LSEQ=TCAACCACTGGAATTCATCA;RSEQ=CTCTCTCTCTGAATGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2329:26:16,10:1450,851:2301,26:0.0112:2,2:32.2:1:34.1:1:0.84165:1.06489:60:25:0.0109:0.0021:0.1 0/0:2382:23:18,5:1506,851:2357,23:0.0097:2,2:43.5:1:35:1:0.19207:2.03:60:46:0.0098:0.0008:0
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chr14 45645955 45645955 A - exonic FANCM . frameshift deletion FANCM:NM_001308133:exon13:c.3920delA:p.V1310Lfs*2,FANCM:NM_020937:exon14:c.3998delA:p.V1336Lfs*2 rs746983128 ID=COSV57496817;OCCURENCE=10(large_intestine),1(NS),5(stomach),1(soft_tissue) . . . . . . . . 0.0001 0.0001 0 0 0 0.0001 0 0.0003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q21.2 0.25 182 2454 chr14 45645954 . CA C 182 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2392;VD=37;AF=0.0155;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0495;SOR=1.5906;LSEQ=CTCAGTTTTCTTTACCAGTG;RSEQ=AAAAAAAGTTATGAGTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2392:37:22,15:1365,988:2353,37:0.0155:2,2:35.2:1:35:1:1:1.06:60:74:0.0155:0.0021:0.1 0/0:2454:24:14,10:1441,986:2427,24:0.0098:2,2:36.2:1:35:1:1:1.04391:60:48:0.0098:0.0012:0.1
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chr14 45653112 45653112 T - intron FANCM NM_020937:exon17:c.4515+7T>-;NM_001308133:exon16:c.4437+7T>- . . rs747887646 ID=COSV57502086;OCCURENCE=3(large_intestine),1(biliary_tract),1(stomach) . . . . . . . 0.0008 0.0003 0.0015 0.0003 0 0.0002 0.0001 0 0 0.0004 0.0013 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q21.2 0.25 158 1373 chr14 45653111 . CT C 158 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1350;VD=23;AF=0.017;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05874;SOR=1.81283;LSEQ=CAGAGTCACTTAAAGGTAAT;RSEQ=TTTTTTTAGTTTCTTTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1350:23:12,11:612,714:1326,23:0.017:2,2:47.2:1:35:1:0.67438:1.27:60:46:0.017:0.0007:0.1 0/0:1373:13:4,9:647,712:1359,13:0.0095:2,2:38.9:1:33.2:1:0.27275:2.04352:60:12:0.0088:0.0007:0.5
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chr14 68331675 68331675 A T intron RAD51B NM_001321819:exon5:c.316-45A>T;NM_001321818:exon5:c.316-45A>T;NM_133510:exon5:c.316-45A>T;NM_002877:exon5:c.316-45A>T;NM_001321810:exon5:c.316-45A>T;NM_001321809:exon5:c.316-45A>T;NM_001321814:exon5:c.316-45A>T;NM_001321817:exon6:UTR5;NM_001321821:exon5:c.316-45A>T;NM_133509:exon5:c.316-45A>T;NM_001321812:exon4:c.316-45A>T;NM_001321815:exon4:c.202-45A>T . . rs1474939 . 1256131 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.9999 0.9993 1 1 1 1 1 1 0.9374 0.9300 0.9614 0.9435 0.9304 0.9908 0.9344 0.9358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 1 224 68 chr14 68331675 . A T 224 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=99;VD=99;AF=1;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGTGATGTTTATCTAAA;RSEQ=AACTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:99:99:69,30:0,0:0,99:1:0,2:37.3:1:33.9:1:1:0:60:23.75:1:0.0101:1.3 1/1:68:68:48,20:0,0:0,68:1:0,2:34.4:1:33.7:1:1:0:60:33:1:0.0147:1.2
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chr14 68944321 68944321 - T intron RAD51B NM_133510:exon11:c.1037-44->T;NM_001321817:exon12:c.680-44->T . . rs767573044 ID=COSV66852473;OCCURENCE=1(biliary_tract) . . . . . . . 0.0094 0.0138 0.0062 0.0122 0.0065 0.0015 0.0088 0.0132 0.0444 0.0004 0.0001 0 0 0.0006 0.0023 0.0002 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.5 256 1628 chr14 68944321 . A AT 256 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1637;VD=167;AF=0.102;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.01882;SOR=1.29812;LSEQ=AGTTAGTGCATTTCATAACA;RSEQ=TTTTTTTTTTTCAAACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1637:167:113,54:825,366:1191,167:0.102:2,2:40.5:1:34.8:1:0.72072:1.07712:60:334:0.1465:0.0086:0.1 0/1:1628:131:88,42:820,392:1212,131:0.0805:2,2:39.2:1:34.8:1:1:1.00:60:262:0.1098:0.0086:0.2
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chr14 68944344 68944344 T - intron RAD51B NM_133510:exon11:c.1037-21T>-;NM_001321817:exon12:c.680-21T>- . . rs567396898 ID=COSV66846050;OCCURENCE=3(liver) . . . . . 0.295727 0.2282 . 0.3360 0.3425 0.3321 0.2970 0.3355 0.3338 0.3428 0.3573 0.0168 0.0315 0.0307 0.0130 0.0007 0.0434 0.0071 0.0119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.5 295 1863 chr14 68944343 . CT C 295 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1891;VD=342;AF=0.1809;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.15528;SOR=0.9155;LSEQ=TTTTTTTTTTCAAACTTTCT;RSEQ=TTTTTTTTTTTTTCCTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1891:342:217,125:852,478:1330,342:0.1809:2,2:42.7:1:34.9:1:0.84989:1.02674:60:684:0.181:0.0116:0.1 0/1:1863:362:251,111:815,477:1292,362:0.1943:2,2:42:1:34.8:1:0.02967:1.32:60:724:0.195:0.0102:0.2
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chr14 69061180 69061180 - T intron RAD51B NM_133509:exon11:c.1037-22->T . . rs770263514 . . . . . . . . . 4.308e-05 0.0002 0 0 0 6.264e-05 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.25 160 2344 chr14 69061180 . C CT 160 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=2333;VD=24;AF=0.0103;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21484;SOR=1.34306;LSEQ=AGGGCCTAGACTTTGACTTC;RSEQ=TTTTTTTTCTCTCTCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2333:24:12,11:1206,890:2096,24:0.0103:2,2:47.7:1:35:0:0.67355:1.242:60:48:0.0117:0:0.1 0/0:2344:18:7,11:1253,963:2216,18:0.0077:2,2:36.7:1:35:1:0.15516:2.04402:60:36:0.0082:0.0009:0.1
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chr14 69149593 69149593 T - intronic RAD51B . . . . . . . . . . . . . . . . . . . . . 0.0482 0.0959 0.0285 0.025 0 0.0861 0.0191 0.0287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.5 246 873 chr14 69149592 . CT C 246 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=953;VD=127;AF=0.1333;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.13596;SOR=0.85554;LSEQ=CCTTTGAGTATCTCACAAGG;RSEQ=TTTTTTTTTTTAATAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:953:127:89,38:517,290:807,127:0.1333:2,2:39.1:1:34.7:1:0.19517:1.31:60:254:0.1337:0.0157:0.5 0/1:873:133:98,35:487,233:720,133:0.1523:2,2:39.4:1:34.9:1:0.18666:1.34:60:266:0.1532:0.0218:0.5
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chr14 69149628 69149628 T - intron RAD51B NM_001321818:exon11:c.1037-26T>- . . . . . . . . . . . . . . . . . . . . 0.0503 0.0772 0.0677 0.0325 0.0757 0.0125 0.0332 0.0337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.5 294 1048 chr14 69149627 . CT C 294 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1131;VD=353;AF=0.3121;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.02207;SOR=1.2146;LSEQ=TAAAAATCTGTAGCTTATGG;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1131:353:203,150:286,163:449,353:0.3121:2,2:43.2:1:34.8:1:0.08029:1.29606:60:706:0.3138:0.0168:0.5 0/1:1048:285:165,120:271,144:415,285:0.2719:2,2:42.4:1:34.5:1:0.04781:1.36804:60:284:0.2726:0.0162:0.5
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chr14 69149790 69149790 - A UTR3 RAD51B NM_001321818:c.*129_*130insA . . . ID=COSV72159326;OCCURENCE=1(oesophagus) . . . . . . . . . . . . . . . . 3.927e-05 0.0001 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.25 105 804 chr14 69149790 . G GA 105 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Insertion;DP=915;VD=4;AF=0.0044;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13667;SOR=0.43709;LSEQ=CCTGTTATTTTTTTCTGTCA;RSEQ=AAAAAAAATGGGGCCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:915:4:3,1:464,364:828,4:0.0044:2,2:22.8:1:35:0:0.63534:2.35:60:8:0.0052:0:1 0/1:804:8:5,3:446,313:759,8:0.01:2,2:40.9:1:35:1:1:1.17:60:16:0.0109:0.0012:0.5
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chr14 69149814 69149814 C T UTR3 RAD51B NM_001321818:c.*153C>T . . rs4899251 . . . . . . 0.875599 0.7609 . . . . . . . . . 0.9117 0.8947 0.8681 0.9184 0.7168 0.9477 0.9402 0.9223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.5 294 794 chr14 69149814 . C T 294 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=877;VD=353;AF=0.4025;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10611;SOR=1.13943;LSEQ=AAAAATGGGGCCTGCCAAAA;RSEQ=GTACTGTAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:877:353:189,164:286,236:522,353:0.4025:2,2:40:1:34.8:1:0.72983:1.05148:60:706:0.4095:0.0057:1.1 0/1:794:295:172,123:286,213:499,295:0.3715:2,2:40.1:1:34.8:1:0.82364:1.04:60:294:0.3774:0.0101:1.1
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chr14 69149822 69149822 A - UTR3 RAD51B NM_001321818:c.*161delA . . rs10710408 . . . . . . 0.59365 0.5655 . . . . . . . . . 0.6533 0.5223 0.6672 0.7390 0.5245 0.7460 0.7284 0.7124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.1 0.5 292 769 chr14 69149821 . TA T 292 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=860;VD=331;AF=0.3849;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.02807;SOR=1.22479;LSEQ=GGGCCTGCCAAAACGTACTG;RSEQ=AAAAAAAAAAAAATCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:860:331:171,160:241,196:437,331:0.3849:2,2:42.6:1:35:1:0.34317:1.15028:60:662:0.3858:0.0209:0.7 0/1:769:260:150,110:236,188:424,260:0.3381:2,2:43:1:35:1:0.63395:1.09:60:520:0.3385:0.0117:0.8
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chr14 75483812 75483812 T C exonic MLH3 . synonymous SNV MLH3:NM_014381:exon12:c.4263A>G:p.Q1421Q,MLH3:NM_001040108:exon13:c.4335A>G:p.Q1445Q rs13712 . 255063 Hereditary_nonpolyposis_colorectal_cancer_type_7|not_specified|not_provided MONDO:MONDO:0013725,MedGen:C1858380,OMIM:614385|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.580072 0.8393 0.5019 0.5671 0.4437 0.7703 0.8277 0.5325 0.5338 0.5274 0.4976 0.5295 0.4433 0.7076 0.4570 0.8401 0.5384 0.5341 0.5491 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.3 1 382 2146 chr14 75483812 . T C 382 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2247;VD=2237;AF=0.9955;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13531;SOR=1.68017;LSEQ=GGCTCACAGGGAGGCATGGA;RSEQ=TGCTGCAGGCTCTGCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2247:2237:1402,835:0,0:0,2237:0.9955:0,2:42.3:1:34.4:1:1:0:60:92.208:0.9964:0.0058:1.1 1/1:2146:2130:1313,817:0,1:1,2130:0.9925:0,2:41.2:1:34.6:1:0.38386:0:60:212:0.9958:0.0056:1.1
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chr14 75485489 75485489 A G intron MLH3 NM_001040108:exon12:c.4242+43T>C;NM_014381:exon11:c.4170+43T>C . . rs175053 . 1282168 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.990615 1 0.9889 0.9969 0.9663 0.9984 1 1 0.9999 0.9986 0.9999 0.9903 0.9664 0.9988 1 1 1 0.9999 0.9969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.3 1 370 1827 chr14 75485489 . A G 370 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1827;VD=1824;AF=0.9984;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04586;SOR=3.34551;LSEQ=AAGCCAGAAAAGAAAGAGAA;RSEQ=ATAAACTTTGCTCCCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1827:1824:1224,600:0,0:0,1824:0.9984:0,2:38.8:1:34.2:1:1:0:60:61.897:0.9994:0.0378:1.3 1/1:1827:1817:1227,590:0,0:0,1817:0.9945:0,2:39.6:1:34.5:1:1:0:60:112.562:0.9967:0.0432:1.3
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chr14 75497429 75497429 A - intron MLH3 NM_001040108:exon9:c.3828-24T>-;NM_014381:exon8:c.3756-24T>- . . rs767006941 ID=COSV53153317;OCCURENCE=1(stomach),1(large_intestine),1(biliary_tract) 485656 not_specified MedGen:CN169374 no_assertion_criteria_provided Likely_benign . . 0.0417 0.1341 0.0810 0.1531 0.0779 0.0256 0.1259 0.1404 0.2530 0.0032 0.0014 0.0081 0 0 0.0230 0.0023 0.0028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.3 0.5 280 2095 chr14 75497428 . TA T 280 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1966;VD=231;AF=0.1175;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.26008;SOR=0.93554;LSEQ=AAAGAGATAACCTCAAATGT;RSEQ=AAAAAAAAAAGAGTGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1966:231:100,131:745,957:1702,231:0.1175:2,2:44.2:1:34.9:1:0.94367:1.01979:60:462:0.1177:0.0031:0.1 0/1:2095:261:111,150:791,1011:1802,261:0.1246:2,2:45.2:1:34.9:1:0.68929:1.05728:60:522:0.1246:0.0062:0.1
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chr14 75513883 75513883 T C exonic MLH3 . nonsynonymous SNV MLH3:NM_001040108:exon2:c.2476A>G:p.N826D,MLH3:NM_014381:exon2:c.2476A>G:p.N826D rs175081 . 255065 Hereditary_nonpolyposis_colorectal_cancer_type_7|not_specified|not_provided MONDO:MONDO:0013725,MedGen:C1858380,OMIM:614385|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.990415 1 0.9888 0.9969 0.9662 0.9983 1 1 0.9999 0.9986 0.9999 0.9902 0.9660 0.9988 1 0.9994 1 0.9999 0.9969 0.848 0.028 T 0.345 0.139 N 1 0.182 P 0 0.065 N -1.3 0.800 T -0.26 0.112 N -0.969 0.374 T 0.000 0.000 T . . . . . 0.050 0.106 N c -1.500 -1.443 1.000 0.462 0.651 0.465 0 1.33 0.209 0.319 0.191 -0.152 0.108 0.000 0.063 0.019 0.132 3.716 0.079 . . . 14q24.3 1 401 3097 chr14 75513883 . T C 401 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2987;VD=2971;AF=0.9946;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38874;SOR=0.84324;LSEQ=GAATGGAAACTTCTCTGAGT;RSEQ=AAGGATGTGGCTTGCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2987:2971:1567,1404:0,0:0,2971:0.9946:0,2:38:1:34.4:1:1:0:60:117.84:0.9956:0.0278:1.1 1/1:3097:3083:1655,1428:1,0:1,3083:0.9955:0,2:37:1:34.6:1:1:0:60:153.15:0.9964:0.0429:1.1
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chr14 75514338 75514338 T - exonic MLH3 . frameshift deletion MLH3:NM_001040108:exon2:c.2021delA:p.N674Ifs*6,MLH3:NM_014381:exon2:c.2021delA:p.N674Ifs*6 . ID=COSV53152383;OCCURENCE=1(NS),1(stomach),1(prostate),11(large_intestine) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.3 0.5 200 2698 chr14 75514337 . AT A 200 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2660;VD=51;AF=0.0192;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.41286;SOR=0.93934;LSEQ=TAACTTATATTCGTTCTGCA;RSEQ=TTTTTTTGTTGGGCAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2660:51:25,26:1313,1296:2609,51:0.0192:2,2:38.2:1:34.9:1:0.88826:1.05364:60:102:0.0192:0.003:0.2 0/1:2698:55:32,23:1332,1311:2643,55:0.0204:2,2:40:1:34.6:1:0.27732:1.37:60:54:0.0201:0.0033:0.1
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chr14 75514603 75514603 - T exonic MLH3 . frameshift insertion MLH3:NM_001040108:exon2:c.1755dupA:p.E586Rfs*3,MLH3:NM_014381:exon2:c.1755dupA:p.E586Rfs*3 rs751465048 ID=COSV53154152;OCCURENCE=3(large_intestine),1(NS),1(skin) 995970 Hereditary_nonpolyposis_colorectal_cancer_type_7 MONDO:MONDO:0013725,MedGen:C1858380,OMIM:614385 criteria_provided,_single_submitter Uncertain_significance . . . 3.799e-05 0 0 0 0 1.854e-05 0 0.0002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q24.3 0.5 198 2286 chr14 75514603 . C CT 198 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=2259;VD=51;AF=0.0226;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39628;SOR=1.07689;LSEQ=TCTTCCACAATTGCTAGATT;RSEQ=TTTTTTTTTCTCTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2259:51:29,22:974,1006:1980,51:0.0226:2,2:40.6:1:35:1:0.32147:1.36:60:102:0.0266:0.0022:0.1 0/1:2286:48:27,21:986,1020:2006,48:0.021:2,2:37.5:1:34.7:1:0.38158:1.33:60:96:0.0244:0.0026:0.2
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chr14 105242073 105242075 CTC - exonic AKT1 . nonframeshift deletion AKT1:NM_001014431:exon5:c.349_351del:p.E117del,AKT1:NM_005163:exon5:c.349_351del:p.E117del,AKT1:NM_001014432:exon6:c.349_351del:p.E117del rs768025881 ID=COSV62573212;OCCURENCE=3(NS),1(haematopoietic_and_lymphoid_tissue) 841150 Cowden_syndrome_6 MONDO:MONDO:0014048,MedGen:C3554519,OMIM:615109 criteria_provided,_single_submitter Uncertain_significance . . . 9.424e-06 0 8.93e-05 0 0 0 0 0 3.238e-05 0.0001 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14q32.33 0.25 182 3623 chr14 105242072 . TCTC T 182 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=3542;VD=32;AF=0.009;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.34873;SOR=0.88361;LSEQ=TGAGCCCGACCGGAAGTCCA;RSEQ=CTCCTCCTCCTGCTTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3542:32:16,16:1793,1714:3507,32:0.009:2,2:40.3:1:35:1:1:1.04609:60:64:0.0091:0.0008:0.2 0/1:3623:37:18,19:1852,1734:3586,37:0.0102:2,2:42.7:1:35:1:0.74341:1.12735:60:74:0.0103:0.0006:0.2
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chr15 32972396 32972397 TT - intronic ARHGAP11A-SCG5;SCG5 . . . rs201959683 . . . . . . 0.559704 0.5387 . . . . . . . . . 0.4699 0.3502 0.5129 0.5938 0.3602 0.3193 0.5608 0.4871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q13.3 0.5 309 1416 chr15 32972395 . CTT C 309 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1371;VD=495;AF=0.3611;SHIFT3=17;MSI=19.000;MSILEN=1;SSF=0.27652;SOR=1.05138;LSEQ=ACTTTTCTGCACTTGCTACT;RSEQ=TTTTTTTTTTTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1371:495:237,258:87,94:181,495:0.3611:2,2:45.7:1:34.5:1:1:1.00753:60:494:0.3616:0.0292:0.2 0/1:1416:495:235,260:102,113:215,495:0.3496:2,2:44.6:1:34.6:1:1:1.00:60:494:0.3494:0.036:0.3
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chr15 33015825 33015825 T - intronic GREM1 . . . . . . . . . . . . . . . . . . . . . 9.785e-05 0 0 0 0 0 0.0002 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q13.3 0.25 105 741 chr15 33015824 . CT C 105 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=749;VD=8;AF=0.0107;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19811;SOR=1.98831;LSEQ=TTTGAGGAAAATGTACTTTT;RSEQ=TTAAAAAAAAAAAAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:8:7,1:492,249:741,8:0.0107:2,2:32.9:1:35:1:0.28015:3.54:60:16:0.0107:0.004:0.4 0/0:741:4:2,2:450,287:737,4:0.0054:2,2:34.8:1:35:0:0.6454:1.56691:60:8:0.0054:0:0
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chr15 33015828 33015828 A - intronic GREM1 . . . rs35877271 . 1263203 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.910743 0.9563 . . . . . . . . . 0.8576 0.7340 0.8599 0.8731 0.9955 0.7177 0.9281 0.8765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q13.3 0.5 307 781 chr15 33015827 . TA T 307 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=803;VD=453;AF=0.5641;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.29576;SOR=0.94213;LSEQ=GAGGAAAATGTACTTTTCTT;RSEQ=AAAAAAAAAAAAAAGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:803:453:307,146:84,35:119,453:0.5641:2,2:43.3:1:34.9:1:0.58164:1.14107:60:452:0.5678:0.061:0.1 1/0:781:452:273,179:73,33:106,452:0.5787:2,2:43.7:1:35:1:0.11981:1.4495:60:904:0.581:0.0538:0.1
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chr15 43739686 43739686 - A intron TP53BP1 NM_001141979:exon13:c.2717-3->T;NM_001141980:exon13:c.2717-3->T;NM_005657:exon13:c.2702-3->T;NM_001355001:exon13:UTR5 . . rs753702168 ID=COSV55506284;OCCURENCE=1(oesophagus),1(central_nervous_system) . . . . . . . . 0.1188 0.0887 0.1934 0.1203 0.0628 0.0992 0.112 0.1767 0.0749 0.0408 0.2013 0.1702 0.0843 0 0.0898 0.1223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q15.3 0.5 229 345 chr15 43739686 . G GA 229 PASS STATUS=AFDiff;SAMPLE=NCCL202312;TYPE=Insertion;DP=375;VD=100;AF=0.2667;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.29578;SOR=1.11213;LSEQ=TGAAATGAAATGGGGTTTCT;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:100:56,44:100,88:188,100:0.2667:2,2:45.2:1:34.5:1:0.70981:1.12:60:99:0.6346:0:0.3 0/1:345:85:56,29:66,94:160,85:0.2464:2,2:48:1:34.9:1:0.00028:2.74:60:170:0.5629:0:0.2
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chr15 43739703 43739703 G A intron TP53BP1 NM_001141979:exon13:c.2717-20C>T;NM_001141980:exon13:c.2717-20C>T;NM_005657:exon13:c.2702-20C>T;NM_001355001:exon13:UTR5 . . rs376055109 . . . . . . . . . 1.705e-05 0 0.0002 0 0 0 0 0 0.0016 0.0006 0.0023 0 0.0014 0.0064 0.0018 0.0033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q15.3 0.25 87 272 chr15 43739703 . G A 87 PASS STATUS=StrongLOH;SAMPLE=NCCL202312;TYPE=SNV;DP=296;VD=0;AF=0;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.00262;SOR=0;LSEQ=TCTGAAAAAAAAAAAAAAAA;RSEQ=AAAAAAGAAAGAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:155,140:295,0:0:2,0:37.8:1:26.7:1:1:0:60:3.338:1:0:0.3 0/1:272:8:4,4:119,143:262,8:0.0294:2,2:15.6:1:29:1:1:1.20:60:3:0.0249:0:1.6
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chr15 51502844 51502844 A C ncRNA_intronic MIR4713HG . . . rs4646 ID=COSV53058004;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) 339355 Aromatase_deficiency|not_provided MONDO:MONDO:0013301,MedGen:C1960539,OMIM:613546,Orphanet:ORPHA91|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.664337 0.7034 . 0.7080 0.7201 0.5580 0.7119 0.7459 0.7478 0.7271 0.6468 0.7183 0.6890 0.5191 0.7649 0.6846 0.7235 0.7476 0.7244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q21.2 0.5 347 2054 chr15 51502844 . A C 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2135;VD=1027;AF=0.481;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07369;SOR=0.91259;LSEQ=TGTGAACAGGAGCAGATGAC;RSEQ=AATAGCACCTAGCTTGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2135:1027:574,453:630,478:1108,1027:0.481:2,2:39.3:1:34.6:1:0.66245:1.04016:60:113.111:0.4788:0.0136:1.1 1/0:2054:1035:611,424:579,438:1017,1035:0.5039:2,2:39.6:1:34.7:1:0.34768:1.09:60:146.857:0.5027:0.0161:1.1
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chr15 66745890 66745890 G A intronic MAP2K1 . . . rs7169326 . . . . . . 0.983227 1 . 0.9989 0.9439 1 1 . 0.9996 1 1 0.9869 0.9543 0.9976 1 1 1 0.9998 0.9969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q22.31 1 365 1398 chr15 66745890 . G A 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1447;VD=1445;AF=0.9986;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51292;SOR=0.5173;LSEQ=GCAAGCAGCACAGTGAGTAG;RSEQ=TGATTCCTGGAAACCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1447:1445:798,647:0,0:0,1445:0.9986:0,2:42.9:1:34.8:1:1:0:60:360.25:0.9986:0.0214:1.1 1/1:1398:1397:758,639:0,0:0,1397:0.9993:0,2:42:1:34.7:1:1:0:60:348.25:1:0.0293:1.1
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chr15 88423463 88423463 C T intron NTRK3 NM_002530:exon18:c.2292+38G>A;NM_001012338:exon19:c.2334+38G>A;NM_001243101:exon17:c.2268+38G>A . . rs1560975 ID=COSV62295880;OCCURENCE=1(large_intestine),2(central_nervous_system) 1238173 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.446885 0.6081 0.4777 0.5393 0.2132 0.5377 0.6048 0.5756 0.6141 0.5403 0.4267 0.4879 0.2176 0.5407 0.6258 0.6006 0.5777 0.6026 0.5429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 1 365 1538 chr15 88423463 . C T 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1461;VD=1456;AF=0.9966;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59124;SOR=0.94977;LSEQ=CTGAGATAGCTCTTATGAGC;RSEQ=CTCCCCCAATCAAGATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1461:1456:936,520:0,0:0,1456:0.9966:0,2:37.1:1:34.1:1:1:0:60:52.926:0.9993:0.0281:1.1 1/1:1538:1533:993,540:1,0:1,1533:0.9967:0,2:37.7:1:34.5:1:1:0:60:138.364:0.9987:0.0202:1.1
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chr15 88478798 88478800 AGA - intronic NTRK3 . . . rs951091341 . . . . . . . . . . . . . . . . . 6.472e-05 0.0001 0 0 0 0 6.676e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 0.5 213 2917 chr15 88478797 . CAGA C 213 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=3122;VD=68;AF=0.0218;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.51784;SOR=0.99257;LSEQ=GTGGTTTATTTATTTTCATG;RSEQ=AGAAGAAGAAGAAGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3122:68:41,27:1973,1074:3047,68:0.0218:2,2:35.1:1:35:1:0.44427:1.20968:60:136:0.0218:0.0048:0.2 0/1:2917:64:38,26:1904,942:2846,64:0.0219:2,2:37.8:1:34.8:1:0.22744:1.38284:60:128:0.022:0.0031:0.2
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chr15 88479928 88479928 T C intronic NTRK3 . . . rs920068 . . . . . . 0.9998 1 . . . . . . . . . 1.0000 1 1 1 1 1 0.9999 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 1 389 2543 chr15 88479928 . T C 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2370;VD=2361;AF=0.9962;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01141;SOR=2.49881;LSEQ=CACACACACGCACGCACACA;RSEQ=GCACACCTATCAACCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2370:2361:1340,1021:0,2:2,2361:0.9962:0,2:39.2:1:34.6:1:0.18732:0:60:195.75:0.9962:0.0148:1.1 1/1:2543:2519:1440,1079:2,2:4,2519:0.9906:2,2:37.1:1:34.5:1:1:1.33:60:131.579:0.9932:0.037:1.1
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chr15 88481200 88481200 A - intronic NTRK3 . . . rs759550145 . . . . . . . . . . . . . . . . . 0.0202 0.0233 0.0192 0.0216 0 0.0424 0.0184 0.0275 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 0.5 278 1972 chr15 88481199 . GA G 278 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2063;VD=229;AF=0.111;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05522;SOR=0.85228;LSEQ=GAGTATGAAATGACAGAGAC;RSEQ=AAAAAAAAAAGGAAAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2063:229:170,59:1281,500:1781,229:0.111:2,2:40.8:1:34.7:1:0.48186:1.12:60:458:0.1114:0.0165:0.1 0/1:1972:252:186,66:1218,458:1676,252:0.1278:2,2:39.5:1:34.9:1:0.76142:1.06:60:504:0.128:0.0142:0.1
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chr15 88576383 88576383 T - intronic NTRK3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 0.5 121 763 chr15 88576382 . CT C 121 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=713;VD=11;AF=0.0154;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.27073;SOR=1.47841;LSEQ=GTTCCCATCACAAACATTTT;RSEQ=TTTTTTTACTTTTGGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:713:11:3,8:161,541:702,11:0.0154:2,2:20.2:1:35:1:0.72164:1.26:60:22:0.0154:0.0028:0.3 0/1:763:8:1,7:150,605:755,8:0.0105:2,2:25:1:35:0:1:1.73446:60:16:0.0105:0:0.4
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chr15 88679785 88679785 G A exonic NTRK3 . synonymous SNV NTRK3:NM_001320134:exon6:c.678C>T:p.N226N,NTRK3:NM_001320135:exon6:c.384C>T:p.N128N,NTRK3:NM_001007156:exon8:c.678C>T:p.N226N,NTRK3:NM_001012338:exon8:c.678C>T:p.N226N,NTRK3:NM_001243101:exon8:c.678C>T:p.N226N,NTRK3:NM_002530:exon8:c.678C>T:p.N226N rs1863480 ID=COSV58135005;OCCURENCE=1(thyroid) . . . . . 0.998203 1 0.9958 0.9969 0.9992 0.9965 1 0.9968 0.9958 0.9957 0.9985 0.9971 0.9995 0.9988 0.9967 1 0.9977 0.9951 0.9969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 1 391 2383 chr15 88679785 . G A 391 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2346;VD=2334;AF=0.9949;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48484;SOR=0.902;LSEQ=CCATTGCAAGTGATAACAGC;RSEQ=TTGTCACCCTCTCGTACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2346:2334:1221,1113:0,0:0,2334:0.9949:0,2:40.1:1:34.9:1:1:0:60:465.8:0.9991:0.0175:1.1 1/1:2383:2372:1277,1095:0,0:0,2372:0.9954:0,2:39.8:1:34.9:1:1:0:60:592:0.9987:0.0218:1.1
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chr15 88680684 88680684 G A exonic NTRK3 . synonymous SNV NTRK3:NM_001320134:exon5:c.573C>T:p.N191N,NTRK3:NM_001320135:exon5:c.279C>T:p.N93N,NTRK3:NM_001007156:exon7:c.573C>T:p.N191N,NTRK3:NM_001012338:exon7:c.573C>T:p.N191N,NTRK3:NM_001243101:exon7:c.573C>T:p.N191N,NTRK3:NM_002530:exon7:c.573C>T:p.N191N rs1128994 ID=COSV58119651;OCCURENCE=1(skin),2(lung) 1216197 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.270767 0.2222 0.3032 0.2607 0.3733 0.1499 0.2213 0.2412 0.2700 0.2616 0.2698 0.2928 0.3753 0.1838 0.3709 0.2398 0.2457 0.2692 0.2454 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15q25.3 0.5 359 2483 chr15 88680684 . G A 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2558;VD=1256;AF=0.491;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28183;SOR=1.03474;LSEQ=GGAAGCTGGGAGCCATCAGC;RSEQ=TTGATGCAGTAGAGGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2558:1256:735,521:739,557:1296,1256:0.491:2,2:39.9:1:34.9:1:0.44664:1.06:60:313:0.4941:0.0121:1.1 0/1:2483:1198:694,504:761,517:1278,1198:0.4825:2,2:40:1:34.8:1:0.4377:1.06893:60:1197:0.4844:0.0117:1.1
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chr16 23615043 23615043 A - intronic PALB2 . . . rs35294437 . 1220188 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . 0.4114 0.3810 0.3841 0.4203 0.3875 0.3936 0.4254 0.4483 0.1286 0.1456 0.1343 0.0865 0.1800 0.3091 0.0923 0.1489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16p12.2 0.5 284 1322 chr16 23615042 . TA T 284 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1420;VD=289;AF=0.2035;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.47875;SOR=1.00966;LSEQ=TTACATATCCAAAAAACAAT;RSEQ=AAAAAAAAAAAAAGGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1420:289:130,159:508,533:1041,289:0.2035:2,2:39.6:1:34.8:1:0.25851:1.16557:60:578:0.2038:0.0148:0.2 0/1:1322:267:113,154:472,500:972,267:0.202:2,2:43.4:1:35:1:0.07236:1.28625:60:534:0.2024:0.0068:0.2
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chr16 23618610 23618610 T - intronic PALB2 . . . rs11356162 . . . . . . 0.727037 0.7798 . . . . . . . . . 0.5661 0.4675 0.5575 0.6650 0.6024 0.4087 0.6331 0.5888 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16p12.2 0.5 278 880 chr16 23618609 . AT A 278 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=917;VD=234;AF=0.2552;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.03979;SOR=0.82606;LSEQ=GTTCATTACTCTTTATGTGA;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:234:125,109:223,242:465,234:0.2552:2,2:48.9:1:34.9:1:0.17432:1.24:60:468:0.2555:0.0044:0.1 0/1:880:258:107,151:190,217:407,258:0.2932:2,2:45.6:1:34.8:1:0.20074:1.23523:60:516:0.2942:0.0216:0.1
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chr16 23624964 23624964 C T intronic PALB2 . . . rs249934 . . . . . . 0.348842 0.3512 . . . . . . . . . 0.3250 0.4384 0.2725 0.2601 0.3657 0.3429 0.2547 0.2875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16p12.2 0.5 300 1514 chr16 23624964 . C T 300 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1501;VD=455;AF=0.3031;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15101;SOR=1.08946;LSEQ=AACAAGAGCAAAACTCCATC;RSEQ=CAAAAAAAAAAAAAAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1501:455:327,128:524,247:771,455:0.3031:2,2:41:1:34:1:0.1585:1.20:60:64:0.3166:0:1.1 0/1:1514:432:294,138:556,248:804,432:0.2853:2,2:38.4:1:34.2:1:0.69971:1.05229:60:53:0.2992:0.0112:1.1
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chr16 23624966 23624966 A - intronic PALB2 . . . rs770083033 . . . . . . . . . . . . . . . . . 0.0130 0.0030 0.0417 0.0248 0 0.1592 0.0086 0.0264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16p12.2 0.5 262 1415 chr16 23624965 . CA C 262 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1480;VD=185;AF=0.125;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.08758;SOR=1.17827;LSEQ=ACAAGAGCAAAACTCCATCC;RSEQ=AAAAAAAAAAAAAGTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1480:185:130,55:820,365:1185,185:0.125:2,2:33.1:1:34.9:1:0.79759:1.05:60:370:0.13:0.0331:0.2 0/1:1415:153:105,48:780,358:1138,153:0.1081:2,2:43.6:1:34.9:1:1:1.00:60:306:0.1123:0.0028:0.2
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chr16 23646142 23646144 TCA - splicing PALB2 NM_024675:exon4:r.spl . . rs368593832 ID=COSV55164779;OCCURENCE=1(large_intestine) 132127 Familial_cancer_of_breast MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006 no_assertion_criteria_provided Likely_benign . . . 0.0005 0.0002 0.0008 0.0011 0 0.0003 0.0058 0.0006 0.0002 0.0005 0.0012 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16p12.2 0.5 197 1564 chr16 23646141 . TTCA T 197 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1505;VD=29;AF=0.0193;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=0.01714;SOR=0.59503;LSEQ=GCAAATAGTAATTGTTAACT;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1505:29:17,12:1039,431:1470,29:0.0193:2,2:36.9:1:35:1:0.21573:1.70099:60:58:0.0193:0.0033:0.1 0/1:1564:50:41,9:1128,382:1510,50:0.032:2,2:43.5:1:35:1:0.31905:1.54:60:100:0.032:0.0045:0.1
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chr16 68771348 68771350 GCT - exonic CDH1 . nonframeshift deletion CDH1:NM_001317184:exon1:c.30_32del:p.L15del,CDH1:NM_004360:exon1:c.30_32del:p.L15del rs761309816 ID=COSV99028365;OCCURENCE=1(stomach) 791633 Hereditary_diffuse_gastric_cancer MONDO:MONDO:0007648,MedGen:C1708349,OMIM:137215,Orphanet:ORPHA26106 criteria_provided,_single_submitter Likely_benign . . 0.0044 0.0054 0.01 0.0156 0.0056 0 0.0050 0 0.0053 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q22.1 0.5 202 2299 chr16 68771347 . CGCT C 202 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2522;VD=59;AF=0.0234;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.46743;SOR=1.03511;LSEQ=TTGGAGCCGCAGCCTCTCGG;RSEQ=GCTGCTGCTGCTGCAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2522:59:33,26:1302,1157:2459,59:0.0234:2,2:39.6:1:34.4:1:0.69344:1.13:60:58:0.0234:0.0024:1.1 0/1:2299:52:28,24:1185,1054:2239,52:0.0226:2,2:40:1:34.9:1:1:1.04:60:104:0.023:0.0013:1.2
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chr16 68771372 68771372 C T intron CDH1 NM_001317184:exon1:c.48+6C>T;NM_001317186:exon1:UTR5;NM_001317185:exon1:UTR5;NM_004360:exon1:c.48+6C>T . . rs3743674 ID=COSV55733220;OCCURENCE=1(breast),1(liver),16(meninges),1(large_intestine),2(central_nervous_system),1(lung) 140395 Malignant_tumor_of_prostate|Hereditary_diffuse_gastric_cancer|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|Blepharocheilodontic_syndrome_1|not_specified|not_provided Human_Phenotype_Ontology:HP:0012125,MONDO:MONDO:0008315,MedGen:C0376358,OMIM:176807,SNOMED_CT:399068003|MONDO:MONDO:0007648,MedGen:C1708349,OMIM:137215,Orphanet:ORPHA26106|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MONDO:MONDO:0054740,MedGen:C4551988,OMIM:119580|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.763379 0.7688 0.8603 0.8095 0.6579 0.7019 0.7172 0.7576 0.8779 0.8043 0.7862 0.7976 0.6539 0.7548 0.9367 0.7605 0.8241 0.8757 0.8388 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q22.1 1 381 1986 chr16 68771372 . C T 381 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2171;VD=2164;AF=0.9968;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56509;SOR=0.93679;LSEQ=CTGCTGCTGCTGCAGGTACC;RSEQ=CGGATCCCCTGACTTGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2171:2164:1043,1121:0,0:0,2164:0.9968:0,2:39.4:1:34.4:1:1:0:60:93.087:0.9972:0.0101:1.2 1/1:1986:1980:925,1055:0,0:0,1980:0.997:0,2:38.3:1:34.5:1:1:0:60:164:0.998:0.0257:1.2
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chr16 68857441 68857441 T C exonic CDH1 . synonymous SNV CDH1:NM_001317184:exon12:c.1893T>C:p.A631A,CDH1:NM_001317186:exon12:c.111T>C:p.A37A,CDH1:NM_001317185:exon13:c.528T>C:p.A176A,CDH1:NM_004360:exon13:c.2076T>C:p.A692A rs1801552 ID=COSV55728161;OCCURENCE=13(meninges),1(large_intestine),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue) 152484 Malignant_tumor_of_prostate|Hereditary_diffuse_gastric_cancer|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|Blepharocheilodontic_syndrome_1|not_specified|not_provided Human_Phenotype_Ontology:HP:0012125,MONDO:MONDO:0008315,MedGen:C0376358,OMIM:176807,SNOMED_CT:399068003|MONDO:MONDO:0007648,MedGen:C1708349,OMIM:137215,Orphanet:ORPHA26106|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MONDO:MONDO:0054740,MedGen:C4551988,OMIM:119580|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.71865 0.6448 0.7161 0.6556 0.8897 0.6693 0.6404 0.5823 0.6237 0.6066 0.6616 0.6961 0.8838 0.6615 0.5927 0.6658 0.5878 0.6235 0.6365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q22.1 0.5 346 2173 chr16 68857441 . T C 346 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2262;VD=1082;AF=0.4783;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31631;SOR=0.96991;LSEQ=TGTGACTGTGAAGGGGCCGC;RSEQ=GGCGTCTGTAGGAAGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2262:1082:635,447:702,468:1170,1082:0.4783:2,2:38.7:1:34.4:1:0.54779:1.05585:60:97.364:0.4775:0.0155:1.1 0/1:2173:1056:635,421:668,433:1101,1056:0.486:2,2:38.9:1:34.4:1:0.82574:1.02281:60:116.333:0.4858:0.0225:1.1
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chr16 69143577 69143577 A G exonic HAS3 . synonymous SNV HAS3:NM_001199280:exon2:c.279A>G:p.A93A,HAS3:NM_005329:exon2:c.279A>G:p.A93A,HAS3:NM_138612:exon2:c.279A>G:p.A93A rs2232228 ID=COSV54707058;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(lung) . . . . . 0.342252 0.5149 0.3264 0.3943 0.1129 0.4208 0.4726 0.3697 0.4369 0.4263 0.3602 0.3388 0.1234 0.4055 0.4967 0.4770 0.3728 0.4304 0.4027 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q22.1 0.5 368 3228 chr16 69143577 . A G 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3328;VD=1605;AF=0.4823;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09932;SOR=0.93732;LSEQ=GTGGCACTGTGCATTGCCGC;RSEQ=TACCAGGAGGACCCTGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3328:1605:850,755:891,829:1720,1605:0.4823:2,2:39.5:1:34.6:1:0.50933:1.05:60:159.5:0.4819:0.0087:1.1 0/1:3228:1609:877,732:865,748:1613,1609:0.4985:2,2:39.3:1:34.6:1:0.62082:1.04:60:200.125:0.4986:0.022:1.1
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chr16 89805261 89805261 A G intron FANCA NM_001286167:exon42:c.4264+29T>C;NM_000135:exon42:c.4260+29T>C . . rs1800359 ID=COSV57066846;OCCURENCE=4(large_intestine),1(haematopoietic_and_lymphoid_tissue),4(upper_aerodigestive_tract) 255966 Fanconi_anemia,_complementation_group_A|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.850839 0.9901 0.6991 0.7126 0.9348 0.8086 0.9870 0.6928 0.5916 0.6700 0.8028 0.7261 0.9243 0.7458 0.5066 0.9852 0.6773 0.6005 0.6776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 1 393 2659 chr16 89805261 . A G 393 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2737;VD=2709;AF=0.9898;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18037;SOR=0.73328;LSEQ=TCAATTCTCATGTCCCCCAC;RSEQ=TGGCCCAAGGTGGGCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2737:2709:1440,1269:2,0:2,2709:0.9898:0,2:37.1:1:34.5:1:0.50185:0:60:122.136:0.9937:0.0303:1.1 1/1:2659:2639:1386,1253:2,0:2,2639:0.9925:0,2:37.1:1:34.5:1:0.50112:0:60:124.667:0.9943:0.0282:1.1
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chr16 89805977 89805977 G A intron FANCA NM_001286167:exon40:c.3935-16C>T;NM_000135:exon40:c.3935-16C>T . . rs1061646 ID=COSV57068489;OCCURENCE=1(breast) 255968 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.538139 0.7073 0.3475 0.4218 0.5415 0.5633 0.7131 0.5435 0.2810 0.3359 0.4573 0.4091 0.5340 0.5680 0.2367 0.7338 0.3808 0.3033 0.4002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 339 1715 chr16 89805977 . G A 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1773;VD=852;AF=0.4805;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30403;SOR=0.96362;LSEQ=GAGGTCTGCAACACCAAGAA;RSEQ=TGGCTCAGGCAACTCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1773:852:387,465:398,521:919,852:0.4805:2,2:42.9:1:34.9:1:0.38895:1.09:60:851:0.483:0.0096:1.1 0/1:1715:840:388,452:381,493:874,840:0.4898:2,2:43.3:1:34.8:1:0.28554:1.11:60:419:0.4903:0.0099:1.1
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chr16 89831510 89831510 C A intron FANCA NM_001286167:exon28:c.2602-36G>T;NM_000135:exon28:c.2602-36G>T . . rs2159116 ID=COSV59796461;OCCURENCE=2(lung),1(upper_aerodigestive_tract) 255984 Fanconi_anemia,_complementation_group_A|not_specified MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.0932508 0.003 0.1267 0.1506 0.0360 0.0997 0.0029 0.1349 0.1928 0.1657 0.1859 0.1159 0.0345 0.1136 0.1854 0.0043 0.1481 0.1660 0.1258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 336 1972 chr16 89831510 . C A 336 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1924;VD=866;AF=0.4501;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19845;SOR=1.05833;LSEQ=ACCCGGCCGTTTCTTCATTG;RSEQ=GCAAGTTTCACTGTGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1924:866:359,507:472,584:1056,866:0.4501:2,2:41.3:1:34.5:1:0.1651:1.14133:60:215.5:0.4539:0.0182:1.1 0/1:1972:860:376,484:471,633:1104,860:0.4361:2,2:40.7:1:34.3:1:0.64632:1.04:60:77.182:0.4361:0.0132:1.1
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chr16 89836323 89836323 C T exonic FANCA . nonsynonymous SNV FANCA:NM_000135:exon26:c.2426G>A:p.G809D,FANCA:NM_001286167:exon26:c.2426G>A:p.G809D rs7195066 ID=COSV59796193;OCCURENCE=1(large_intestine),10(soft_tissue) 137993 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.666733 0.9881 0.4307 0.4798 0.6776 0.6824 0.9864 0.4287 0.3049 0.4506 0.5903 0.4758 0.6626 0.5800 0.2583 0.9796 0.3961 0.3317 0.4488 0.528 0.072 T 0.250 0.155 N 1 0.090 P -0.345 0.033 N -1.85 0.843 D -0.03 0.075 N -1.008 0.274 T 0.000 0.000 T . . . . . 0.022 0.064 N c -1.616 -1.622 0.220 0.183 0.707 0.730 0 -0.167 0.126 0.077 0.145 -1.145 0.017 0.000 0.063 0.000 0.016 2.369 0.040 . ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000204991.6|ENSG00000258947.2|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000204991.6|ENSG00000260259.1|ENSG00000204991.6|ENSG00000003249.9|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000158792.11|ENSG00000204991.6 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Pancreas|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Testis|Testis|Thyroid|Uterus|Whole_Blood|Whole_Blood 16q24.3 0.5 355 2415 chr16 89836323 . C T 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2519;VD=1239;AF=0.4919;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40951;SOR=1.01477;LSEQ=CAGGGACAGGAAGGCCAGCA;RSEQ=CAGGTGCAGGAGGACCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2519:1239:744,495:744,529:1273,1239:0.4919:2,2:39.2:1:34.6:1:0.41701:1.07:60:246.8:0.4934:0.0111:1.1 0/1:2415:1179:733,446:770,464:1234,1179:0.4882:2,2:40.4:1:34.5:1:0.93304:1.00972:60:106.182:0.4887:0.0046:1.1
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chr16 89838078 89838078 A G intron FANCA NM_001286167:exon23:c.2151+8T>C;NM_000135:exon23:c.2151+8T>C . . rs1800340 ID=COSV66881670;OCCURENCE=1(breast) 255987 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.559904 0.7242 0.3743 0.4437 0.5216 0.6672 0.7576 0.4244 0.3027 0.4092 0.5743 0.4106 0.5094 0.5692 0.2567 0.7345 0.3960 0.3151 0.4264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 339 1884 chr16 89838078 . A G 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1927;VD=943;AF=0.4894;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3586;SOR=0.97475;LSEQ=CTGCTTTGTTCTGAGCCCCT;RSEQ=CACCTACCATGTGTTCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1927:943:637,306:648,330:978,943:0.4894:2,2:37.2:1:34.4:1:0.56082:1.06:60:116.875:0.489:0.0166:1.1 0/1:1884:934:635,299:675,270:945,934:0.4958:2,2:38:1:34.6:1:0.10828:1.17706:60:232.5:0.4952:0.0037:1.1
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chr16 89845194 89845194 A G intron FANCA NM_001286167:exon20:c.1826+15T>C;NM_000135:exon20:c.1826+15T>C . . rs1800337 . 255991 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.682508 0.9871 0.4882 0.5207 0.6910 0.6902 0.9852 0.4838 0.3729 0.4726 0.5944 0.5225 0.6752 0.6005 0.3079 0.9790 0.4579 0.4010 0.4959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 314 1192 chr16 89845194 . A G 314 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1208;VD=597;AF=0.4942;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44932;SOR=1.01383;LSEQ=GAAGTAGTCATCCCCTTCTA;RSEQ=CCGTTGCTGCATACCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1208:597:425,172:436,173:609,597:0.4942:2,2:37.9:1:34.1:1:0.89867:1.01994:60:65.333:0.4908:0.0149:1.3 0/1:1192:585:426,159:459,144:603,585:0.4908:2,2:39.4:1:34.6:1:0.20607:1.18952:60:96.5:0.4898:0.0168:1.3
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chr16 89849480 89849480 C T exonic FANCA . nonsynonymous SNV FANCA:NM_000135:exon16:c.1501G>A:p.G501S,FANCA:NM_001286167:exon16:c.1501G>A:p.G501S rs2239359 ID=COSV66881058;OCCURENCE=1(kidney),11(soft_tissue) 137983 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.624002 0.8671 0.4823 0.5068 0.6878 0.6398 0.8518 0.5583 0.3982 0.4869 0.4903 0.5222 0.6818 0.5742 0.35 0.8375 0.5413 0.3945 0.4764 1.0 0.010 T 0.309 0.040 N 1 0.090 P -1.245 0.008 N -1.65 0.827 D 1.48 0.008 N -0.957 0.398 T 0.000 0.000 T . . . . . 0.016 0.050 N c -1.909 -1.880 0.029 0.139 0.719 0.830 0 -4.64 0.031 -0.965 0.039 -0.863 0.028 0.000 0.063 0.012 0.117 14.543 0.675 Fanconi anaemia group A protein, N-terminal domain ENSG00000185324.17|ENSG00000261373.1|ENSG00000075399.8|ENSG00000185324.17|ENSG00000003249.9|ENSG00000185324.17|ENSG00000185324.17|ENSG00000185324.17|ENSG00000075399.8|ENSG00000131165.10|ENSG00000258839.2|ENSG00000185324.17|ENSG00000131165.10|ENSG00000185324.17|ENSG00000075399.8|ENSG00000185324.17|ENSG00000258839.2|ENSG00000185324.17|ENSG00000075399.8|ENSG00000185324.17|ENSG00000258839.2|ENSG00000185324.17|ENSG00000075399.8|ENSG00000258839.2|ENSG00000075399.8|ENSG00000131165.10|ENSG00000185324.17|ENSG00000075399.8|ENSG00000204991.6|ENSG00000185324.17|ENSG00000075399.8|ENSG00000258839.2|ENSG00000185324.17|ENSG00000261373.1|ENSG00000075399.8|ENSG00000185324.17|ENSG00000158792.11|ENSG00000261373.1|ENSG00000141002.14 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Coronary|Artery_Tibial|Brain_Cortex|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Left_Ventricle|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Whole_Blood|Whole_Blood|Whole_Blood|Whole_Blood 16q24.3 1 375 1682 chr16 89849480 . C T 375 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1770;VD=1756;AF=0.9921;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4447;SOR=1.12859;LSEQ=GAGGAGGGAGCGGTACTTGC;RSEQ=GGGAACCAGGGGTGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1770:1756:895,861:0,1:1,1756:0.9921:0,2:41.9:1:34.8:1:0.49061:0:60:438:0.9977:0.0362:1.2 1/1:1682:1667:885,782:0,1:1,1667:0.9911:0,2:42.6:1:34.7:1:0.46942:0:60:276.833:0.9952:0.0065:1.2
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chr16 89857964 89857964 T C intron FANCA NM_001286167:exon14:c.1226-20A>G;NM_000135:exon14:c.1226-20A>G . . rs1800330 ID=COSV66881251;OCCURENCE=2(upper_aerodigestive_tract) 256000 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.571885 0.7341 0.3907 0.4489 0.5597 0.6709 0.7665 0.4218 0.3046 0.4133 0.5727 0.4208 0.5416 0.5728 0.2467 0.7447 0.3912 0.3170 0.4236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 346 2078 chr16 89857964 . T C 346 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2139;VD=1043;AF=0.4876;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14191;SOR=1.07033;LSEQ=TCTAGTTAAGAACCATGACA;RSEQ=AGTCACAGCAAGGCAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2139:1043:500,543:527,564:1091,1043:0.4876:2,2:40.6:1:34.6:1:0.89657:1.01475:60:114.889:0.4861:0.0159:1.7 0/1:2078:978:448,530:531,564:1095,978:0.4706:2,2:40.7:1:34.8:1:0.23417:1.11376:60:977:0.4706:0.0144:1.7
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chr16 89858505 89858505 T C intron FANCA NM_001286167:exon13:c.1084-29A>G;NM_000135:exon13:c.1084-29A>G . . rs6500452 ID=COSV66880734;OCCURENCE=1(breast),1(upper_aerodigestive_tract) 256002 Fanconi_anemia,_complementation_group_A|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.531749 0.7292 0.3700 0.4224 0.5154 0.6624 0.7629 0.4071 0.2928 0.3862 0.4807 0.4009 0.4994 0.5680 0.2351 0.7413 0.3770 0.3067 0.3969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 339 1850 chr16 89858505 . T C 339 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1779;VD=834;AF=0.4688;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50397;SOR=0.99845;LSEQ=AAAGCATCCGCTCCCTTCAA;RSEQ=ATCCAAGCAAACCAATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1779:834:325,509:390,552:942,834:0.4688:2,2:42.9:1:34.7:1:0.30883:1.10646:60:138:0.4678:0.0112:1.9 0/1:1850:868:304,564:405,577:982,868:0.4692:2,2:41.7:1:34.8:1:0.00632:1.30202:60:216:0.4696:0.0119:1.9
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chr16 89858525 89858525 C G intron FANCA NM_001286167:exon13:c.1084-49G>C;NM_000135:exon13:c.1084-49G>C . . rs1800287 ID=COSV66881254;OCCURENCE=2(upper_aerodigestive_tract) 256003 Fanconi_anemia,_complementation_group_A|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.702676 0.9871 0.5118 0.5267 0.7609 0.6939 0.9852 0.4780 0.3736 0.4725 0.5912 0.5441 0.7515 0.6026 0.2980 0.9796 0.4495 0.4029 0.4969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 325 1566 chr16 89858525 . C G 325 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1508;VD=717;AF=0.4755;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42191;SOR=1.01699;LSEQ=TATCCAAGCAAACCAATGTG;RSEQ=GACAGATGACCCCTCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1508:717:246,471:285,504:789,717:0.4755:2,2:40.8:1:34.3:1:0.48283:1.08262:60:88.625:0.4758:0.0186:2.1 0/1:1566:738:235,503:311,513:824,738:0.4713:2,2:40.6:1:34.2:1:0.01674:1.29738:60:72.8:0.4706:0.0307:2.1
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chr16 89866043 89866043 T C exonic FANCA . nonsynonymous SNV FANCA:NM_001351830:exon8:c.700A>G:p.T234A,FANCA:NM_000135:exon9:c.796A>G:p.T266A,FANCA:NM_001018112:exon9:c.796A>G:p.T266A,FANCA:NM_001286167:exon9:c.796A>G:p.T266A rs7190823 . 138033 Malignant_tumor_of_breast|Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.690495 0.9871 0.5060 0.5255 0.7279 0.6963 0.9854 0.4805 0.3761 0.4697 0.5919 0.5344 0.7087 0.6062 0.3079 0.9802 0.4539 0.4064 0.5020 1.0 0.010 T 0.417 0.129 N 1 0.090 P -2.125 0.001 N 1.19 0.376 T 1.66 0.006 N -1.001 0.295 T 0.000 0.000 T . . . . . 0.003 0.017 N c -1.528 -1.404 0.056 0.150 0.707 0.730 0 1.85 0.243 0.671 0.247 0.069 0.176 0.056 0.214 0.024 0.140 5.109 0.140 Fanconi anaemia group A protein, N-terminal domain ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000221819.2|ENSG00000187741.10|ENSG00000187741.10|ENSG00000204991.6|ENSG00000185324.17|ENSG00000158792.11|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000187741.10|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000187741.10|ENSG00000204991.6|ENSG00000204991.6|ENSG00000260259.1|ENSG00000187741.10|ENSG00000204991.6|ENSG00000185324.17|ENSG00000204991.6|ENSG00000158792.11|ENSG00000204991.6 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Brain_Frontal_Cortex_BA9|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Pancreas|Pancreas|Skin_Sun_Exposed_Lower_leg|Testis|Testis|Testis|Thyroid|Uterus|Whole_Blood|Whole_Blood 16q24.3 0.5 329 1616 chr16 89866043 . T C 329 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1562;VD=731;AF=0.468;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12672;SOR=0.91977;LSEQ=TCTCTGCAGTACATCAACCG;RSEQ=GACCTGTCAAAATAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1562:731:369,362:435,394:829,731:0.468:2,2:40.6:1:34:1:0.44657:1.08306:60:44.688:0.4628:0.0102:1.3 0/1:1616:790:394,396:453,370:823,790:0.4889:2,2:41.5:1:34.2:1:0.04088:1.23037:60:59.769:0.4859:0.0149:1.2
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chr16 89869761 89869761 T C intron FANCA NM_001286167:exon8:c.710-12A>G;NM_000135:exon8:c.710-12A>G;NM_001351830:exon7:c.614-12A>G;NM_001018112:exon8:c.710-12A>G . . rs1800286 . 256006 Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified|not_provided MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.842851 0.9911 0.6958 0.7093 0.9240 0.8075 0.9893 0.6798 0.5900 0.6734 0.7985 0.7226 0.9146 0.7404 0.5132 0.9852 0.6640 0.6020 0.6759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 1 353 1174 chr16 89869761 . T C 353 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1081;VD=1077;AF=0.9963;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.45491;SOR=0.68991;LSEQ=GAACAAAATCTGAAAAACCA;RSEQ=AAAACCAAAGTTATTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1081:1077:406,671:0,0:0,1077:0.9963:0,2:40.2:1:34.5:1:1:0:60:88.75:0.9981:0.0426:1.1 1/1:1174:1171:489,682:0,1:1,1171:0.9974:0,2:41.3:1:34.7:1:1:0:60:291.75:0.9983:0.0366:1.1
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chr16 89882807 89882807 G T intronic FANCA . . . rs78004870 ID=COSV66882105;OCCURENCE=1(central_nervous_system),1(thyroid) 1220908 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.573682 0.9821 . 1 . . . . . . 1 0.4218 0.4841 0.5377 0.2447 0.9770 0.4014 0.3258 0.4236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 338 2883 chr16 89882807 . G T 338 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3140;VD=1606;AF=0.5115;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37756;SOR=1.01758;LSEQ=CCGCGCCGCCCCAGCCGGGC;RSEQ=CCCACCCCGCACAGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3140:1606:934,672:910,611:1521,1606:0.5115:2,2:36.8:1:31.8:1:0.3446:1.07154:60:11.646:0.4997:0.0226:2.1 1/0:2883:1462:901,561:891,514:1405,1462:0.5071:2,2:37.3:1:32.3:1:0.33478:1.0793:60:16.405:0.5024:0.0146:2.1
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chr16 89882826 89882826 C T intronic FANCA . . . rs72631431 . 1215829 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.573682 0.9821 . 0.7 . 0.5 . . . . 0.7083 0.4226 0.4851 0.5362 0.2448 0.9770 0.3957 0.3287 0.4211 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16q24.3 0.5 358 2899 chr16 89882826 . C T 358 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3193;VD=1634;AF=0.5117;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.48392;SOR=0.99662;LSEQ=CGCCCACCCCGCACAGCCCC;RSEQ=CGGGCGCGGCGTCCGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3193:1634:938,696:926,626:1552,1634:0.5117:2,2:37.5:1:33.6:1:0.20805:1.09756:60:43.162:0.5109:0.0257:2 1/0:2899:1486:886,600:887,521:1408,1486:0.5126:2,2:37.6:1:33.4:1:0.0669:1.15287:60:31.304:0.5096:0.0283:2
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chr17 7572155 7572155 A - UTR3 TP53 NM_001276697:c.*772delT;NM_001276696:c.*1061delT;NM_001276698:c.*1061delT;NM_001126117:c.*973delT;NM_001126116:c.*1061delT;NM_001126115:c.*772delT;NM_001126114:c.*1061delT;NM_000546:c.*772delT;NM_001276761:c.*772delT;NM_001126112:c.*772delT;NM_001126118:c.*772delT;NM_001126113:c.*973delT;NM_001276699:c.*973delT;NM_001276760:c.*772delT;NM_001276695:c.*973delT . . rs200757381 . 346161 Li-Fraumeni_syndrome MONDO:MONDO:0018875,MedGen:C0085390,OMIM:PS151623,Orphanet:ORPHA524,SNOMED_CT:428850001 criteria_provided,_single_submitter Uncertain_significance . . . . . . . . . . . 0.6331 0.7270 0.6114 0.5714 0.5388 0.4443 0.6100 0.5816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17p13.1 0.5 265 556 chr17 7572154 . GA G 265 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=579;VD=208;AF=0.3592;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.45581;SOR=1.02167;LSEQ=GACCCAGTCTCAAAGAAAAA;RSEQ=AAAAAAAAAAAAAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:208:172,36:214,55:269,208:0.3592:2,2:37.3:1:34.5:1:0.41246:1.23:60:416:0.3611:0.0656:0.3 0/1:556:197:154,43:212,59:271,197:0.3543:2,2:47.3:1:34.8:1:1:1.00329:60:196:0.3538:0.0018:0.3
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chr17 7578645 7578645 C T intron TP53 NM_001126117:c.-112G>A;NM_001126116:c.-112G>A;NM_001126115:c.-112G>A . . rs2909430 ID=COSV52668782;OCCURENCE=1(upper_aerodigestive_tract),13(large_intestine),2(central_nervous_system) 433983 Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.842851 0.9762 . . . . . . . . . 0.8407 0.7388 0.9125 0.8333 0.9597 0.8823 0.8719 0.8665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17p13.1 0.5 351 2139 chr17 7578645 . C T 351 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2227;VD=1114;AF=0.5002;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46261;SOR=0.99251;LSEQ=GCAGCAAAGAAACAAACATG;RSEQ=GTAAGCACCTCCTGCAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2227:1114:598,516:594,518:1112,1114:0.5002:2,2:38.7:1:34.7:1:0.93227:1.01:60:277.5:0.5059:0.0126:1.1 1/0:2139:1074:605,469:552,510:1062,1074:0.5021:2,2:39.4:1:34.6:1:0.04579:1.19:60:152.429:0.5062:0.0047:1.2
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chr17 7578712 7578714 TTT - intron TP53 NM_001126117:c.-179_-181delAAA;NM_001126116:c.-179_-181delAAA;NM_001126115:c.-179_-181delAAA . . rs141204613 . 791833 Squamous_cell_carcinoma_of_the_head_and_neck|not_provided MONDO:MONDO:0010150,MeSH:D000077195,MedGen:C1168401,OMIM:275355,SNOMED_CT:716659002|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign . . . . . . . . . . . 0.7765 0.6850 0.7236 0.7542 0.9579 0.6384 0.8291 0.7767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17p13.1 0.5 296 1385 chr17 7578711 . CTTT C 296 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1454;VD=382;AF=0.2627;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.25615;SOR=1.06181;LSEQ=TCTACACCTCAGGAGCTTTT;RSEQ=TTTTTTTTTTTTTTTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1454:382:158,224:228,308:536,382:0.2627:2,2:44.2:1:34.6:1:0.73491:1.04945:60:94.5:0.2605:0.0213:0.8 0/1:1385:348:135,213:187,304:491,348:0.2513:2,2:42.2:1:34.8:1:0.88544:1.03:60:696:0.2511:0.0296:0.8
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chr17 7579472 7579472 G C exonic TP53 . nonsynonymous SNV TP53:NM_001126118:exon3:c.98C>G:p.P33R,TP53:NM_000546:exon4:c.215C>G:p.P72R,TP53:NM_001126112:exon4:c.215C>G:p.P72R,TP53:NM_001126113:exon4:c.215C>G:p.P72R,TP53:NM_001126114:exon4:c.215C>G:p.P72R,TP53:NM_001276695:exon4:c.98C>G:p.P33R,TP53:NM_001276696:exon4:c.98C>G:p.P33R,TP53:NM_001276760:exon4:c.98C>G:p.P33R,TP53:NM_001276761:exon4:c.98C>G:p.P33R rs1042522 ID=COSV52666208;OCCURENCE=5(penis),4(liver),18(meninges),38(large_intestine),3(central_nervous_system),2(biliary_tract),1(pleura),15(bone),1(stomach),1(urinary_tract),21(soft_tissue),3(pancreas),1(skin),1(prostate),2(lung),2(thyroid),3(upper_aerodigestive_tract),1(small_intestine),1(endometrium) 27390 CODON_72_POLYMORPHISM|Li-Fraumeni_syndrome_1|Hereditary_cancer-predisposing_syndrome|Li-Fraumeni_syndrome|Lip_and_oral_cavity_carcinoma|not_specified|not_provided .|Gene:553989,MONDO:MONDO:0007903,MedGen:C1835398,OMIM:151623|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0018875,MedGen:C0085390,OMIM:PS151623,Orphanet:ORPHA524,SNOMED_CT:428850001|MONDO:MONDO:0023644,MedGen:C0220641|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.542931 0.5863 0.6300 0.6550 0.3814 0.7110 0.5938 0.7304 0.7341 0.6580 0.4989 0.6194 0.3853 0.6957 0.7252 0.5447 0.7263 0.7275 0.6916 0.262 0.174 T 0.371 0.044 U 1 0.090 P 1.355 0.339 L -5.23 0.993 D -0.29 0.206 N -0.929 0.444 T 0.000 0.000 T . . . . . 0.361 0.252 N c -0.879 -0.947 1.000 0.403 0.722 0.854 0 1.87 0.244 1.438 0.344 1.045 0.669 0.003 0.159 0.001 0.043 9.773 0.396 . ENSG00000108947.4 Brain_Cerebellum 17p13.1 0.5 359 2899 chr17 7579472 . G C 359 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2843;VD=1393;AF=0.49;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.25305;SOR=1.0372;LSEQ=CTGCTGGTGCAGGGGCCACG;RSEQ=GGGGAGCAGCCTCTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2843:1393:792,601:846,591:1437,1393:0.49:2,2:37.5:1:34.3:1:0.28644:1.08622:60:91.867:0.4923:0.0134:1.1 0/1:2899:1394:816,578:871,620:1491,1394:0.4809:2,2:38.6:1:34.4:1:0.96985:1.00:60:91.933:0.4837:0.0131:1.1
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chr17 7579652 7579659 CTCCAGGT - splicing TP53 NM_001276696:exon3:r.spl;NM_001126114:exon3:r.spl;NM_000546:exon3:r.spl;NM_001276761:exon3:r.spl;NM_001126112:exon3:r.spl;NM_001126118:exon2:r.spl;NM_001126113:exon3:r.spl;NM_001276760:exon3:r.spl;NM_001276695:exon3:r.spl . . rs780090842 ID=COSV99386020;OCCURENCE=10(large_intestine),2(central_nervous_system) . . . . . . . . 0.0002 0 0 0 0 0.0003 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17p13.1 0.5 241 1749 chr17 7579651 . CCTCCAGGT C 241 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1973;VD=124;AF=0.0628;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.23824;SOR=0.90233;LSEQ=CAGCCCCCCAGCCCCCCAGC;RSEQ=CCCCAGCCCTCCAGGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1973:124:81,43:972,737:1709,124:0.0628:2,2:13.2:1:34.7:1:0.07381:1.43:60:248:0.0682:0:0.5 0/1:1749:121:61,60:920,707:1627,121:0.0692:2,2:13.3:1:34.6:1:0.21698:1.27975:60:242:0.0695:0:0.5
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chr17 7579658 7579659 GT CC splicing TP53 NM_001276696:exon3:r.spl;NM_001126114:exon3:r.spl;NM_000546:exon3:r.spl;NM_001276761:exon3:r.spl;NM_001126112:exon3:r.spl;NM_001126118:exon2:r.spl;NM_001126113:exon3:r.spl;NM_001276760:exon3:r.spl;NM_001276695:exon3:r.spl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17p13.1 0.25 150 1713 chr17 7579658 . GT CC 150 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Complex;DP=1911;VD=18;AF=0.0094;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12847;SOR=0.66926;LSEQ=CCAGCCCCCCAGCCCTCCAG;RSEQ=CCCCAGCCCTCCAGGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1911:18:10,8:916,711:1627,18:0.0094:2,2:10.9:1:33.7:1:1:1.03065:60:17:0.0105:0.0016:1.9 0/1:1713:24:11,13:876,690:1566,24:0.014:2,2:10:1:32.8:1:0.40818:1.49999:60:11:0.0141:0.0018:1.9
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chr17 29482977 29482977 - T intron NF1 NM_000267:exon2:c.61-24->T;NM_001128147:exon2:c.61-24->T;NM_001042492:exon2:c.61-24->T . . rs376172637 ID=COSV62202276;OCCURENCE=2(biliary_tract) 915092 not_specified MedGen:CN169374 criteria_provided,_single_submitter Benign . . 0.0302 0.0358 0.0583 0.0379 0.0235 0.0053 0.0285 0.0314 0.0594 0.0091 0.0296 0.0013 0 0 0.0018 0.0006 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 204 763 chr17 29482977 . G GT 204 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=832;VD=60;AF=0.0721;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.30023;SOR=1.13241;LSEQ=TAAGGATAAGCTGTTAACGT;RSEQ=TTTTTTTTTTCTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:832:60:43,16:493,192:685,60:0.0721:2,2:39.1:1:34.6:1:1:1.05:60:120:0.0909:0:0.1 0/1:763:49:37,12:472,157:629,49:0.0642:2,2:42.7:1:35:0:1:1.03:60:98:0.0792:0:0.3
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chr17 29482988 29482988 - T intron NF1 NM_000267:exon2:c.61-13->T;NM_001128147:exon2:c.61-13->T;NM_001042492:exon2:c.61-13->T . . rs748542958 ID=COSV100646162;OCCURENCE=1(stomach) 1188509 not_provided MedGen:CN517202 criteria_provided,_single_submitter Likely_benign . . 0.0084 0.0021 0.0118 0.0022 0.0020 0.0006 0.0010 0 0.0007 0.0032 0.0103 0 0 0 0 7.894e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 165 857 chr17 29482988 . C CT 165 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=947;VD=28;AF=0.0296;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04309;SOR=1.834;LSEQ=TGTTAACGTGTTTTTTTTTT;RSEQ=TTTTTTTTTCAGCTTCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:947:28:22,6:620,243:863,28:0.0296:2,2:26.9:1:34.5:1:0.52539:1.44:60:56:0.0346:0.0106:0.3 0/1:857:14:11,3:588,203:791,14:0.0163:2,2:37.6:1:33.3:1:1:1.27:60:13:0.017:0:0
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chr17 29528406 29528406 - T intron NF1 NM_000267:exon11:c.1186-23->T;NM_001128147:exon11:c.1186-23->T;NM_001042492:exon11:c.1186-23->T . . rs776587991 ID=COSV62194296;OCCURENCE=3(prostate) . . . . . . . 0.0156 0.0058 0.0082 0.0021 0.0023 0.0003 0.0041 0.0089 0.0172 0.0014 0.0029 0.0044 0.0036 0 0.0034 6.999e-05 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 194 828 chr17 29528406 . C CT 194 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=868;VD=41;AF=0.0472;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13705;SOR=0.77154;LSEQ=TTTCTCATAGAAATAATCTG;RSEQ=TTTTTTTTTTCTTTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:868:41:24,16:403,329:732,41:0.0472:2,2:43.6:1:35:0:0.62522:1.22:60:82:0.0605:0:0.2 0/1:828:50:31,19:418,269:687,50:0.0604:2,2:36.6:1:34.4:1:1:1.05:60:100:0.0758:0.0097:0.1
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chr17 29533435 29533435 T - intron NF1 NM_000267:exon12:c.1392+46T>-;NM_001128147:exon12:c.1392+46T>-;NM_001042492:exon12:c.1392+46T>- . . rs757336533 ID=COSV62208566;OCCURENCE=3(stomach),1(upper_aerodigestive_tract),7(large_intestine) . . . . . . . . 2.835e-05 0 0 0 0 3.694e-05 0 6.115e-05 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 175 1240 chr17 29533434 . AT A 175 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1237;VD=27;AF=0.0218;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.30255;SOR=0.84241;LSEQ=TCTCACCTCCTTTCTATTGC;RSEQ=TTTTTTTAGTGTCTTTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1237:27:8,19:472,738:1210,27:0.0218:2,2:41.8:1:35:1:0.42522:1.51848:60:54:0.0218:0.0024:0.1 0/1:1240:32:16,16:492,716:1208,32:0.0258:2,2:44.2:1:35:1:0.36271:1.45:60:64:0.0259:0.0008:0.1
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chr17 29553485 29553485 G A exonic NF1 . synonymous SNV NF1:NM_000267:exon18:c.2034G>A:p.P678P,NF1:NM_001042492:exon18:c.2034G>A:p.P678P rs2285892 ID=COSV62191601;OCCURENCE=1(breast),7(meninges),1(large_intestine),2(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),11(soft_tissue),1(lung) 184580 Neurofibromatosis,_familial_spinal|Café-au-lait_macules_with_pulmonary_stenosis|Neurofibromatosis-Noonan_syndrome|Hereditary_cancer-predisposing_syndrome|Neurofibromatosis,_type_1|not_specified|not_provided MONDO:MONDO:0008078,MedGen:C1834235,OMIM:162210|MONDO:MONDO:0008672,MedGen:C0553586,OMIM:193520,Orphanet:ORPHA3444,SNOMED_CT:403820003|MONDO:MONDO:0011035,MedGen:C2931482,OMIM:601321,Orphanet:ORPHA638|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0018975,MedGen:C0027831,OMIM:162200,Orphanet:ORPHA636,SNOMED_CT:92824003|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.496805 0.5258 0.4163 0.3869 0.6878 0.5133 0.5298 0.3448 0.3005 0.3410 0.3715 0.4369 0.6742 0.4642 0.2770 0.5062 0.3512 0.3198 0.3422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 1 391 2377 chr17 29553485 . G A 391 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2353;VD=2345;AF=0.9966;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28391;SOR=0.61795;LSEQ=GGATGCAGCGGAACCCCCCC;RSEQ=ATTTGCCGACAAGCCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2353:2345:1452,893:1,0:1,2345:0.9966:0,2:37.9:1:34.8:1:1:0:60:233.5:0.9987:0.0361:1.1 1/1:2377:2372:1447,925:1,0:1,2372:0.9979:0,2:37.8:1:34.9:1:1:0:60:2371:0.9992:0.0341:1.1
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chr17 29663614 29663614 - T intron NF1 NM_000267:exon41:c.6085-39->T;NM_001042492:exon42:c.6148-39->T . . rs554294350 . 1236271 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0113818 0.005 . 0.0076 0.0322 0.0063 0.0133 0 0.0061 0 0.0043 0.0196 0.0609 0.0134 0.0132 0.0060 0.0043 0.0043 0.0077 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 156 1335 chr17 29663614 . G GT 156 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1316;VD=22;AF=0.0167;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.41983;SOR=1.1178;LSEQ=GCTAAAACTTTGAGTCCCAT;RSEQ=TTTTTTTTTTTAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1316:22:12,9:689,357:1046,22:0.0167:2,2:40.7:1:35:0:0.48664:1.44701:60:44:0.0217:0:0.1 0/1:1335:20:16,4:752,393:1145,20:0.015:2,2:49.9:1:34.4:1:0.23634:2.09:60:40:0.0176:0:0.2
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chr17 29663625 29663625 - A intron NF1 NM_000267:exon41:c.6085-28->A;NM_001042492:exon42:c.6148-28->A . . rs33925668 ID=COSV62205868;OCCURENCE=2(central_nervous_system),2(stomach) 487681 not_provided MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.34365 0.3919 . 0.2710 0.4012 0.4053 0.3489 0.3096 0.2491 0.2565 0.2147 0.3401 0.4521 0.3945 0.24 0.3869 0.2598 0.2870 0.2864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 334 1390 chr17 29663625 . T TA 334 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1373;VD=833;AF=0.6067;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.06049;SOR=1.13093;LSEQ=GAGTCCCATGTTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1373:833:560,273:125,75:200,833:0.6067:2,2:45.9:1:34.5:1:0.21203:1.23:60:207:1:0.0036:0.1 1/0:1390:802:530,272:151,75:226,802:0.577:2,2:46.8:1:34.7:1:0.87363:1.03323:60:266:1:0:0.1
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chr17 29670190 29670190 C G intron NF1 NM_000267:exon47:c.7126+37C>G;NM_001042492:exon48:c.7189+37C>G . . rs7405740 ID=COSV100646390;OCCURENCE=2(central_nervous_system) 256140 Neurofibromatosis,_type_1|not_specified|not_provided MONDO:MONDO:0018975,MedGen:C0027831,OMIM:162200,Orphanet:ORPHA636,SNOMED_CT:92824003|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.873802 0.9028 0.8831 0.9066 0.8023 0.8824 0.8865 0.9444 0.9144 0.9071 0.9464 0.8878 0.8047 0.9010 0.9536 0.8583 0.9482 0.9217 0.9104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 1 340 978 chr17 29670190 . C G 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1020;VD=1018;AF=0.998;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2605;SOR=0;LSEQ=TAGAATATTTTTATGAAGTA;RSEQ=TATTAAGAAACCAGAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1020:1018:395,623:0,1:1,1018:0.998:0,2:37.9:1:34.1:1:1:0:60:43.261:0.999:0.0373:1.1 1/1:978:978:352,626:0,0:0,978:1:0,2:37.2:1:34.5:1:1:0:60:107.667:1:0.0429:1.1
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chr17 29676105 29676108 TTGT - splicing NF1 NM_000267:exon48:r.spl;NM_001042492:exon49:r.spl . . rs149197458 . 230772 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.0375399 0.001 0.0723 0.0206 0.1075 0.0139 0.0112 0.0107 0.0081 0.0133 0.0063 0.0248 0.0844 0.0109 0 0 0.0009 0.0009 0.0031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 168 1750 chr17 29676104 . CTTGT C 168 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1783;VD=28;AF=0.0157;SHIFT3=22;MSI=6.000;MSILEN=4;SSF=0.25954;SOR=1.25306;LSEQ=GTTCAAAAAATTAATTCTTA;RSEQ=TTGTTTGTTTGTTTGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1783:28:16,12:1171,584:1755,28:0.0157:2,2:46.5:1:35:1:0.31443:1.50353:60:56:0.0157:0.0011:0.4 0/1:1750:22:9,13:1141,586:1727,22:0.0126:2,2:44.6:1:34.5:1:0.02142:2.81068:60:44:0.0126:0.0011:0
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chr17 29685481 29685481 - T intron NF1 NM_000267:exon54:c.7908-17->T;NM_001042492:exon55:c.7971-17->T . . rs748030522 . 1178144 not_provided MedGen:CN517202 criteria_provided,_single_submitter Likely_benign . . . 0.0004 0.0001 0.0009 0.0003 0.0002 0.0003 0 0.0005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q11.2 0.5 188 1612 chr17 29685481 . C CT 188 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1624;VD=26;AF=0.016;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03043;SOR=0.6083;LSEQ=CTAAAATGTTCCTCTGTTGA;RSEQ=TTTTTTTTTCTTTTAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1624:26:16,9:887,548:1435,26:0.016:2,2:43.5:1:34.6:1:1:1.10:60:52:0.0187:0.0006:0 0/1:1612:42:23,18:891,517:1408,42:0.0261:2,2:39.1:1:34.9:1:0.41189:1.34843:60:84:0.0305:0.0037:0.1
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chr17 33433487 33433487 C T exonic RAD51D . nonsynonymous SNV RAD51D:NM_133629:exon3:c.158G>A:p.R53Q,RAD51D:NM_001142571:exon6:c.554G>A:p.R185Q,RAD51D:NM_002878:exon6:c.494G>A:p.R165Q rs4796033 . 151873 Breast-ovarian_cancer,_familial_4|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013669,MedGen:C3280345,OMIM:614291|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.0950479 0.0407 0.1068 0.1616 0.0338 0.3216 0.0465 0.1828 0.1613 0.1505 0.1700 0.1192 0.0296 0.2883 0.2351 0.0420 0.1652 0.1548 0.1554 1.0 0.682 T 0.000 0.559 N 0.999 0.235 P -1.43 0.006 N -0.18 0.658 T 1.62 0.637 N -1.032 0.199 T 0.000 0.000 T . . . . . 0.039 0.091 N c -1.067 -0.830 0.000 0.050 0.732 0.924 0 0.253 0.147 1.179 0.314 0.051 0.162 1.000 0.715 0.997 0.653 8.011 0.293 AAA+ ATPase domain|DNA recombination and repair protein Rad51-like, C-terminal|DNA recombination and repair protein RecA-like, ATP-binding domain|P-loop containing nucleoside triphosphate hydrolase|Rad51/DMC1/RadA;DNA recombination and repair protein Rad51-like, C-terminal|DNA recombination and repair protein RecA-like, ATP-binding domain|P-loop containing nucleoside triphosphate hydrolase ENSG00000005156.7|ENSG00000005156.7 Artery_Tibial|Lung 17q12 1 368 1528 chr17 33433487 . C T 368 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1552;VD=1546;AF=0.9961;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51056;SOR=0.84596;LSEQ=CATGCACCACCTGGATCCTC;RSEQ=GGAGAGCTTCTGCCTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1552:1546:749,797:0,0:0,1546:0.9961:0,2:40.6:1:34.8:1:1:0:60:514.333:0.9987:0.0483:1.1 1/1:1528:1523:715,808:1,1:2,1523:0.9967:2,2:41.3:1:34.8:1:1:1.12998:60:1522:0.9967:0.0425:1.1
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chr17 33445549 33445549 G A exonic RAD51D . synonymous SNV RAD51D:NM_002878:exon3:c.234C>T:p.S78S rs9901455 ID=COSV99338663;OCCURENCE=1(stomach) 184841 Breast-ovarian_cancer,_familial_4|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided MONDO:MONDO:0013669,MedGen:C3280345,OMIM:614291|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.1875 0.2262 0.1585 0.1195 0.3046 0.1008 0.2359 0.1096 0.0880 0.0893 0.0840 0.1624 0.3035 0.1253 0.1556 0.2270 0.1090 0.0906 0.1217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q12 0.5 345 1971 chr17 33445549 . G A 345 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1932;VD=953;AF=0.4933;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28168;SOR=1.03985;LSEQ=CCAGTGGACAGGATGGCAGT;RSEQ=GAGGTCTTCAGTTCCTCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1932:953:605,348:595,380:975,953:0.4933:2,2:41:1:34.8:1:0.27993:1.11:60:475.5:0.4945:0.0124:1.1 0/1:1971:953:614,339:610,406:1016,953:0.4835:2,2:39.2:1:34.9:1:0.04572:1.21:60:475.5:0.4832:0.0147:1.1
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chr17 37657482 37657482 T - intron CDK12 NM_016507:exon6:c.2420-21T>-;NM_015083:exon6:c.2420-21T>- . . rs753291584 ID=COSV70999528;OCCURENCE=1(stomach) . . . . . . . . 6.976e-05 0.0004 0 0.0001 0 1.901e-05 0 0.0002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q12 0.25 125 1127 chr17 37657481 . AT A 125 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1031;VD=12;AF=0.0116;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33517;SOR=1.31523;LSEQ=TTTTTTTTTTCTTGCTTTTA;RSEQ=TTTTTTTCGTCTTTATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1031:12:7,5:739,280:1019,12:0.0116:2,2:45.2:1:35:0:0.32925:1.8838:60:24:0.0117:0:0 0/0:1127:10:8,2:802,315:1117,10:0.0089:2,2:44.4:1:35:1:0.73424:1.57:60:20:0.0089:0.0009:0.1
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chr17 37855834 37855834 C A exonic ERBB2 . nonsynonymous SNV ERBB2:NM_001289936:exon5:c.22C>A:p.P8T rs4252596 ID=COSV54064965;OCCURENCE=5(central_nervous_system),1(stomach),2(soft_tissue) 139258 not_specified MedGen:CN169374 no_assertion_provided not_provided 0.0658946 0.002 . 0.1760 0.0585 0.1333 0 0 0.1550 0.1102 0.1912 0.0832 0.0183 0.0561 0.1523 0.0012 0.0747 0.1301 0.1112 0.809 0.030 T . . . 1 0.090 P . . . -0.85 0.744 T 0.61 0.025 N -1.099 0.042 T 0.004 0.013 T . . . . . 0.051 0.107 N c -1.021 -1.079 1.000 0.428 0.549 0.223 0 -2.17 0.066 -0.015 0.125 -0.226 0.095 0.002 0.151 0.031 0.148 0.634 0.007 . . . 17q12 0.5 304 920 chr17 37855834 . C A 304 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=852;VD=418;AF=0.4906;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31841;SOR=1.05063;LSEQ=TGCCCCGGGGGTCCTGGAAG;RSEQ=CACAAGGTAAACACAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:852:418:200,218:207,224:431,418:0.4906:2,2:41.7:1:34.7:1:1:1.00727:60:208:0.4923:0.0141:1.1 0/1:920:440:201,239:225,253:478,440:0.4783:2,2:43.5:1:34.7:1:0.69134:1.05737:60:219:0.4845:0.0141:1.1
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chr17 37868715 37868715 C T intron ERBB2 NM_001289938:exon12:c.1058+14C>T;NM_001289936:exon13:c.1103+14C>T;NM_001005862:exon12:c.1058+14C>T;NM_001289937:exon9:c.1148+14C>T;NM_004448:exon9:c.1148+14C>T . . rs4252627 ID=COSV54062257;OCCURENCE=1(liver),1(large_intestine),2(central_nervous_system),1(stomach),20(soft_tissue),3(lung) . . . . . 0.444489 0.3988 0.5123 0.6050 0.2227 0.5664 0.3850 0.6813 0.6719 0.6798 0.6849 0.5113 0.2147 0.5573 0.6358 0.3486 0.6793 0.6490 0.6344 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q12 0.5 340 1581 chr17 37868715 . C T 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1749;VD=881;AF=0.5037;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3794;SOR=1.02401;LSEQ=TTGATGGGTAAGAGTGGGCA;RSEQ=GATGACCTGAGACAGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1749:881:448,433:444,420:864,881:0.5037:2,2:40.1:1:34.8:1:0.8481:1.02174:60:880:0.5075:0.0132:1.1 0/1:1581:787:424,363:408,383:791,787:0.4978:2,2:43.3:1:34.5:1:0.36458:1.10:60:261.333:0.4994:0.0032:1.1
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chr17 37873563 37873563 C - intron ERBB2 NM_001289938:exon18:c.1648-10C>-;NM_001289936:exon19:c.1693-10C>-;NM_001005862:exon18:c.1648-10C>-;NM_001289937:exon15:c.1738-10C>-;NM_004448:exon15:c.1738-10C>- . . rs770953167 ID=COSV54083557;OCCURENCE=1(large_intestine),3(stomach) . . . . . . . 0.0070 0.0002 0.0001 0 0 0 0.0002 0 0.0007 3.254e-05 0 0 0 0 0 6.72e-05 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q12 0.5 180 1957 chr17 37873562 . GC G 180 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2032;VD=36;AF=0.0177;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.51548;SOR=1.0201;LSEQ=GCCCCCCACAAATCTTTTCT;RSEQ=CCCCCCCAGGAGGCTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2032:36:24,12:1235,754:1989,36:0.0177:2,2:44.4:1:35:1:0.60851:1.22:60:72:0.0181:0.0015:0.1 0/1:1957:34:16,18:1231,687:1918,34:0.0174:2,2:40.3:1:34.7:1:0.04723:2.01511:60:68:0.0179:0.002:0.1
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chr17 37879762 37879762 G A intron ERBB2 NM_001289936:exon22:c.2041-29G>A;NM_001005862:exon21:c.1996-29G>A;NM_001289937:exon18:c.2086-29G>A;NM_004448:exon18:c.2086-29G>A . . rs903506 ID=COSV54069307;OCCURENCE=1(oesophagus),1(large_intestine),2(central_nervous_system),1(skin),1(lung) . . . . . 0.451278 0.4018 0.5136 0.6151 0.2380 0.5842 0.3946 0.6857 0.6793 0.6860 0.6916 0.5131 0.2208 0.5612 0.6358 0.3480 0.6787 0.6494 0.6376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q12 0.5 362 3048 chr17 37879762 . G A 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3099;VD=1533;AF=0.4947;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33299;SOR=1.02361;LSEQ=TGGGGTCTGCACCGGCCCCC;RSEQ=GCACTGACCCACCACCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3099:1533:915,618:931,623:1554,1533:0.4947:2,2:35.5:1:34.3:1:0.91233:1.00932:60:116.923:0.4984:0.0232:1.2 0/1:3048:1490:924,566:907,634:1541,1490:0.4888:2,2:35.7:1:34.4:1:0.08082:1.14:60:86.647:0.4897:0.02:1.1
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chr17 37884037 37884037 C G exonic ERBB2 . nonsynonymous SNV ERBB2:NM_004448:exon27:c.3508C>G:p.P1170A,ERBB2:NM_001005862:exon30:c.3418C>G:p.P1140A,ERBB2:NM_001289936:exon31:c.3463C>G:p.P1155A rs1058808 ID=COSV54064104;OCCURENCE=2(oesophagus),1(large_intestine),2(central_nervous_system),1(biliary_tract) 137821 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.452077 0.4018 0.5135 0.6062 0.2277 0.5692 0.3800 0.6763 0.6742 0.6853 0.6909 0.5139 0.2211 0.5589 0.6358 0.3504 0.6785 0.6507 0.6357 0.03 0.453 D . . . 0.001 0.810 P 0.695 0.181 N -0.81 0.740 T -2.31 0.513 N -0.881 0.497 T 0.000 0.000 T . . . . . 0.944 0.608 D c 0.423 0.445 1.000 0.747 0.722 0.854 0 5.04 0.672 4.287 0.586 0.934 0.450 1.000 0.715 0.999 0.750 18.007 0.891 . ENSG00000161395.8|ENSG00000264968.1|ENSG00000161395.8|ENSG00000161395.8|ENSG00000161395.8|ENSG00000161395.8|ENSG00000172057.5|ENSG00000131748.11|ENSG00000161395.8|ENSG00000131771.9|ENSG00000161395.8|ENSG00000131771.9|ENSG00000141744.3|ENSG00000161395.8|ENSG00000161395.8|ENSG00000161395.8|ENSG00000161395.8|ENSG00000172057.5|ENSG00000161395.8|ENSG00000141744.3|ENSG00000141736.9|ENSG00000161395.8|ENSG00000161395.8|ENSG00000161395.8|ENSG00000161395.8|ENSG00000141736.9|ENSG00000161395.8|ENSG00000161395.8|ENSG00000073605.14|ENSG00000161395.8|ENSG00000073605.14|ENSG00000172057.5 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Colon_Transverse|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Liver|Lung|Lung|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Pancreas|Pituitary|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Stomach|Stomach|Thyroid|Whole_Blood|Whole_Blood 17q12 0.5 352 2694 chr17 37884037 . C G 352 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2693;VD=1309;AF=0.4861;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0394;SOR=0.90731;LSEQ=CTGGTGCCACTCTGGAAAGG;RSEQ=CCAAGACTCTCTCCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2693:1309:739,570:765,613:1378,1309:0.4861:2,2:37.7:1:34:1:0.64091:1.04:60:67.895:0.4866:0.0238:1.1 1/0:2694:1375:746,629:718,592:1310,1375:0.5104:2,2:38.3:1:33.8:1:0.78616:1.02262:60:75.389:0.5125:0.0275:1.1
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chr17 41223094 41223094 T C exonic BRCA1 . nonsynonymous SNV BRCA1:NM_007297:exon14:c.4696A>G:p.S1566G,BRCA1:NM_007298:exon14:c.1525A>G:p.S509G,BRCA1:NM_007294:exon15:c.4837A>G:p.S1613G,BRCA1:NM_007299:exon15:c.1525A>G:p.S509G,BRCA1:NM_007300:exon16:c.4900A>G:p.S1634G rs1799966 ID=COSV58783381;OCCURENCE=1(breast),1(penis),9(meninges),2(large_intestine),2(central_nervous_system),3(haematopoietic_and_lymphoid_tissue),1(urinary_tract),2(lung),1(thymus) 50266 Breast_carcinoma|Hereditary_breast_and_ovarian_cancer_syndrome|Malignant_tumor_of_breast|Breast-ovarian_cancer,_familial_1|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.355831 0.372 0.2982 0.3534 0.2388 0.3147 0.3769 0.3944 0.3277 0.3732 0.4997 0.3179 0.2330 0.3254 0.3179 0.3669 0.3936 0.3409 0.3673 0.032 0.446 D 0.372 0.135 N 1 0.090 P 1.845 0.488 L -1.93 0.849 D -0.51 0.476 N -1.080 0.074 T 0.000 0.000 T . . . . . 0.031 0.080 N c -0.857 -0.906 0.000 0.029 0.707 0.730 0 1.5 0.219 -0.194 0.095 1.061 0.807 0.000 0.063 0.030 0.147 6.894 0.233 BRCA1, serine-rich domain;BRCT domain ENSG00000108828.11|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000198496.6|ENSG00000012048.15|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000188554.9|ENSG00000175906.4|ENSG00000177469.12|ENSG00000108828.11|ENSG00000198496.6|ENSG00000188554.9|ENSG00000184988.4|ENSG00000175906.4|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000068079.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000012048.15|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000184988.4|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000184988.4|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000267440.1|ENSG00000108828.11|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000236383.3|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000108830.7|ENSG00000198496.6|ENSG00000236383.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000175906.4 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hypothalamus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Liver|Liver|Lung|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Ovary|Pancreas|Pituitary|Pituitary|Prostate|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Small_Intestine_Terminal_Ileum|Small_Intestine_Terminal_Ileum|Spleen|Spleen|Stomach|Stomach|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Thyroid|Uterus|Vagina|Whole_Blood|Whole_Blood 17q21.31 0.5 355 2588 chr17 41223094 . T C 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2605;VD=1314;AF=0.5044;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29427;SOR=1.03208;LSEQ=AGTATGAGCAGCAGCTGGAC;RSEQ=CTGGGCAGATTCTGCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2605:1314:803,511:779,503:1282,1314:0.5044:2,2:36.2:1:34.3:1:0.87218:1.01:60:76.294:0.5027:0.0261:1.1 0/1:2588:1285:764,521:750,548:1298,1285:0.4965:2,2:36.3:1:34.3:1:0.40156:1.07:60:84.667:0.4947:0.0247:1.1
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chr17 41234470 41234470 A G exonic BRCA1 . synonymous SNV BRCA1:NM_007297:exon11:c.4167T>C:p.S1389S,BRCA1:NM_007298:exon11:c.999T>C:p.S333S,BRCA1:NM_007294:exon12:c.4308T>C:p.S1436S,BRCA1:NM_007299:exon12:c.999T>C:p.S333S,BRCA1:NM_007300:exon12:c.4308T>C:p.S1436S rs1060915 ID=COSV58783806;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),1(liver),3(lung),9(meninges),2(large_intestine),2(central_nervous_system) 131241 Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_1|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.336262 0.371 0.2796 0.3470 0.1799 0.3096 0.3741 0.3947 0.3267 0.3689 0.4989 0.3011 0.1748 0.3210 0.3179 0.3675 0.3938 0.3403 0.3620 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 336 1780 chr17 41234470 . A G 336 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1777;VD=882;AF=0.4963;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26777;SOR=1.0448;LSEQ=CGCAGGTCCTCAAGGGCAGA;RSEQ=GAGTCACTTATGATGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1777:882:540,342:526,367:893,882:0.4963:2,2:38.8:1:34.4:1:0.33251:1.10:60:62:0.4926:0.0073:1.1 0/1:1780:864:532,332:540,371:911,864:0.4854:2,2:37.8:1:34.6:1:0.33178:1.10:60:107:0.4847:0.018:1.1
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chr17 41244000 41244000 T C exonic BRCA1 . nonsynonymous SNV BRCA1:NM_007297:exon9:c.3407A>G:p.K1136R,BRCA1:NM_007294:exon10:c.3548A>G:p.K1183R,BRCA1:NM_007300:exon10:c.3548A>G:p.K1183R rs16942 ID=COSV58784397;OCCURENCE=1(breast),9(meninges),4(large_intestine),2(central_nervous_system),1(ovary),3(haematopoietic_and_lymphoid_tissue),1(stomach),14(soft_tissue),2(prostate),2(lung),1(thyroid) 50257 Breast_carcinoma|Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_1|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.352636 0.371 0.2952 0.3530 0.2347 0.3150 0.3793 0.3942 0.3272 0.3739 0.4996 0.3150 0.2277 0.3234 0.3179 0.3652 0.3933 0.3384 0.3648 1.0 0.010 T 0.152 0.179 N 1 0.090 P -0.485 0.027 N -0.35 0.686 T 0.4 0.036 N -1.024 0.224 T 0.000 0.000 T . . . . . 0.017 0.054 N c -1.714 -1.653 0.994 0.335 0.732 0.924 0 -2.35 0.063 -0.319 0.080 -0.417 0.060 0.000 0.063 0.005 0.090 7.827 0.283 . ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000198496.6|ENSG00000012048.15|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000188554.9|ENSG00000175906.4|ENSG00000177469.12|ENSG00000108828.11|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000175906.4|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000068079.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000012048.15|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000184988.4|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000184988.4|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000267440.1|ENSG00000108828.11|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000236383.3|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000236383.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000175906.4 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hypothalamus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Liver|Liver|Lung|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Ovary|Pancreas|Pituitary|Pituitary|Prostate|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Small_Intestine_Terminal_Ileum|Small_Intestine_Terminal_Ileum|Spleen|Spleen|Stomach|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Thyroid|Uterus|Vagina|Whole_Blood|Whole_Blood 17q21.31 0.5 343 2114 chr17 41244000 . T C 343 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1841;VD=868;AF=0.4715;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36953;SOR=0.97696;LSEQ=GACTCCTGCTAAGCTCTCCT;RSEQ=TCTGGACGCTTTTGCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1841:868:437,431:498,474:972,868:0.4715:2,2:38.2:1:34.5:1:0.70889:1.03621:60:123:0.47:0.0141:1.1 0/1:2114:1009:481,528:595,506:1101,1009:0.4773:2,2:38.9:1:34.4:1:0.00351:1.29062:60:71.071:0.4743:0.0175:1.1
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chr17 41244435 41244435 T C exonic BRCA1 . nonsynonymous SNV BRCA1:NM_007297:exon9:c.2972A>G:p.E991G,BRCA1:NM_007294:exon10:c.3113A>G:p.E1038G,BRCA1:NM_007300:exon10:c.3113A>G:p.E1038G rs16941 ID=COSV58786412;OCCURENCE=1(breast),1(penis),3(haematopoietic_and_lymphoid_tissue),9(meninges),1(thymus),1(large_intestine),2(central_nervous_system) 50254 Breast_carcinoma|Hereditary_breast_and_ovarian_cancer_syndrome|Malignant_tumor_of_breast|Breast-ovarian_cancer,_familial_1|Pancreatic_cancer_4|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|Fanconi_anemia,_complementation_group_S|not_specified|not_provided Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0013685,MedGen:C3280442,OMIM:614320|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MONDO:MONDO:0054748,MedGen:C4554406,OMIM:617883|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.335663 0.371 0.2790 0.3468 0.1796 0.3093 0.3740 0.3944 0.3265 0.3699 0.4992 0.3004 0.1749 0.3182 0.3167 0.3654 0.3933 0.3396 0.3609 0.028 0.461 D 0.155 0.178 N 1 0.090 P 2.275 0.649 M -1.24 0.790 T -5.69 0.880 D -1.094 0.049 T 0.000 0.000 T . . . . . 0.050 0.107 N c -0.492 -0.562 0.988 0.312 0.707 0.730 0 -0.974 0.097 -0.149 0.101 0.964 0.580 0.000 0.063 0.952 0.428 6.162 0.195 . ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000188554.9|ENSG00000175906.4|ENSG00000177469.12|ENSG00000108828.11|ENSG00000198496.6|ENSG00000188554.9|ENSG00000184988.4|ENSG00000175906.4|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000068079.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000012048.15|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000236383.3|ENSG00000198496.6|ENSG00000184988.4|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000184988.4|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000267440.1|ENSG00000108828.11|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000236383.3|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000236383.3|ENSG00000188825.9|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000175906.4 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hypothalamus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Liver|Liver|Lung|Lung|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Pancreas|Pituitary|Pituitary|Prostate|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Small_Intestine_Terminal_Ileum|Small_Intestine_Terminal_Ileum|Spleen|Stomach|Testis|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Thyroid|Uterus|Vagina|Whole_Blood|Whole_Blood 17q21.31 0.5 337 1989 chr17 41244435 . T C 337 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1936;VD=990;AF=0.5114;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48632;SOR=1.00424;LSEQ=TAATATTGCTTGAGCTGGCT;RSEQ=CTTTAAAAACATTTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1936:990:553,437:524,422:946,990:0.5114:2,2:35.2:1:33.8:1:0.85482:1.02:60:48.5:0.5079:0.0103:1.1 1/0:1989:1015:557,458:536,431:967,1015:0.5103:2,2:35.8:1:33.8:1:0.82135:1.02258:60:39.6:0.5064:0.0196:1.1
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chr17 41244936 41244936 G A exonic BRCA1 . nonsynonymous SNV BRCA1:NM_007297:exon9:c.2471C>T:p.P824L,BRCA1:NM_007294:exon10:c.2612C>T:p.P871L,BRCA1:NM_007300:exon10:c.2612C>T:p.P871L rs799917 ID=COSV58784386;OCCURENCE=1(breast),1(peritoneum),9(meninges),4(large_intestine),2(central_nervous_system),3(haematopoietic_and_lymphoid_tissue),1(stomach),14(soft_tissue),1(skin),3(prostate),2(lung) 50251 Breast_carcinoma|Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_1|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.54393 0.371 0.4932 0.4143 0.8224 0.3434 0.3742 0.3953 0.3348 0.3905 0.5279 0.4855 0.8070 0.3532 0.3344 0.3668 0.3956 0.3476 0.4010 1.0 0.010 T 0.001 0.394 N 0.996 0.588 P -3.445 0.000 N -0.05 0.634 T 5.74 0.000 N -0.937 0.432 T 0.000 0.000 T . . . . . 0.017 0.053 N c -1.045 -0.666 1.000 0.747 0.707 0.730 0 5.04 0.672 4.247 0.583 0.202 0.252 1.000 0.715 0.979 0.486 9.647 0.389 . ENSG00000108828.11|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000188554.9|ENSG00000175906.4|ENSG00000108828.11|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000068079.3|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000198496.6|ENSG00000184988.4|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000012048.15|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000236383.3|ENSG00000198496.6|ENSG00000184988.4|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000184988.4|ENSG00000236383.3|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000184988.4|ENSG00000198496.6|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000184988.4|ENSG00000236383.3|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000108828.11|ENSG00000108830.7|ENSG00000198496.6|ENSG00000267681.1|ENSG00000188554.9|ENSG00000236383.3|ENSG00000175906.4|ENSG00000267151.2|ENSG00000237888.1|ENSG00000067596.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000236383.3|ENSG00000198496.6|ENSG00000267681.1|ENSG00000198496.6|ENSG00000198496.6|ENSG00000198496.6|ENSG00000175906.4 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hypothalamus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Liver|Liver|Lung|Lung|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Pancreas|Pituitary|Pituitary|Prostate|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Small_Intestine_Terminal_Ileum|Spleen|Spleen|Stomach|Testis|Testis|Thyroid|Thyroid|Uterus|Vagina|Whole_Blood|Whole_Blood 17q21.31 0.5 360 2617 chr17 41244936 . G A 360 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2666;VD=1295;AF=0.4857;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37142;SOR=0.98061;LSEQ=CATTTCCTGGATTTGAAAAC;RSEQ=GAGCAAATGACTGGCGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2666:1295:698,597:743,621:1364,1295:0.4857:2,2:37.7:1:34.9:1:0.78523:1.02333:60:430.667:0.487:0.0176:1.1 0/1:2617:1284:726,558:714,618:1332,1284:0.4906:2,2:37.8:1:34.8:1:0.13531:1.13:60:320:0.4927:0.0183:1.1
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chr17 41245237 41245237 A G exonic BRCA1 . synonymous SNV BRCA1:NM_007297:exon9:c.2170T>C:p.L724L,BRCA1:NM_007294:exon10:c.2311T>C:p.L771L,BRCA1:NM_007300:exon10:c.2311T>C:p.L771L rs16940 ID=COSV58786443;OCCURENCE=1(breast),9(meninges),2(large_intestine),2(central_nervous_system),3(haematopoietic_and_lymphoid_tissue),1(lung) 131092 Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_1|Pancreatic_cancer_4|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|Fanconi_anemia,_complementation_group_S|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0013685,MedGen:C3280442,OMIM:614320|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MONDO:MONDO:0054748,MedGen:C4554406,OMIM:617883|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.335264 0.371 0.2776 0.3460 0.1790 0.3089 0.3749 0.3937 0.3251 0.3674 0.4991 0.2998 0.1749 0.3206 0.3179 0.3657 0.3935 0.3382 0.3609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 342 1950 chr17 41245237 . A G 342 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1897;VD=922;AF=0.486;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06253;SOR=0.90393;LSEQ=ATAATCAGTACCAGGTACCA;RSEQ=TGAAATACTGCTACTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1897:922:495,427:530,440:970,922:0.486:2,2:36.7:1:34.2:1:0.71195:1.03907:60:64.857:0.4835:0.038:1.1 1/0:1950:997:524,473:488,456:944,997:0.5113:2,2:38.9:1:34.4:1:0.71625:1.04:60:123.625:0.5122:0.0282:1.1
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chr17 41245466 41245466 G A exonic BRCA1 . synonymous SNV BRCA1:NM_007297:exon9:c.1941C>T:p.S647S,BRCA1:NM_007294:exon10:c.2082C>T:p.S694S,BRCA1:NM_007300:exon10:c.2082C>T:p.S694S rs1799949 ID=COSV58784419;OCCURENCE=1(breast),9(meninges),2(large_intestine),2(central_nervous_system),3(haematopoietic_and_lymphoid_tissue),1(stomach),13(soft_tissue),3(lung) 131074 Hereditary_breast_and_ovarian_cancer_syndrome|Breast-ovarian_cancer,_familial_1|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided MONDO:MONDO:0003582,MeSH:D061325,MedGen:C0677776,OMIM:PS604370,Orphanet:ORPHA145|MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.336462 0.371 0.2957 0.3522 0.2354 0.3146 0.3748 0.3940 0.3262 0.3728 0.4998 0.3160 0.2290 0.3234 0.3179 0.3676 0.3938 0.3392 0.3661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 347 1961 chr17 41245466 . G A 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1893;VD=927;AF=0.4897;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17373;SOR=0.93932;LSEQ=TTCAGCTCTGGGAAAGTATC;RSEQ=CTGTCATGTCTTTTACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1893:927:467,460:507,458:965,927:0.4897:2,2:40.4:1:34.7:1:0.35764:1.09034:60:308:0.4981:0.0122:1.1 1/0:1961:991:498,493:501,466:967,991:0.5054:2,2:39.9:1:34.9:1:0.49792:1.06427:60:990:0.5093:0.0066:1.1
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chr17 41248589 41248589 A - intronic BRCA1 . . . rs34226398 . 259582 Breast-ovarian_cancer,_familial_1|not_provided MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MedGen:CN517202 reviewed_by_expert_panel Benign 0.432907 0.3869 . . . . . . . . . 0.4606 0.5174 0.4322 0.4308 0.4617 0.2778 0.4280 0.44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 277 799 chr17 41248588 . CA C 277 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=841;VD=248;AF=0.2949;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.24693;SOR=0.92381;LSEQ=ACAGGGCAAGACCCCGTCTC;RSEQ=AAAAAAAAAAAAAAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:841:248:145,103:180,148:328,248:0.2949:2,2:41.9:1:34.6:1:0.39747:1.16:60:496:0.2956:0.0428:0.2 0/1:799:249:142,107:198,111:309,249:0.3116:2,2:42.4:1:34.8:1:0.09757:1.34338:60:498:0.3124:0.0463:0.2
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chr17 41250047 41250047 - T intronic BRCA1 . . . rs35771473 . . . . . . . . . . . . . . . . . 0.2824 0.2148 0.345 0.3119 0.3706 0.2202 0.3116 0.3305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 284 1114 chr17 41250047 . C CT 284 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1140;VD=292;AF=0.2561;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.46751;SOR=0.98759;LSEQ=GAATTCTGAGCTCAGCAGCT;RSEQ=TTTTTTTTTTTTTTTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1140:292:118,173:261,270:531,292:0.2561:2,2:47.6:1:34.7:1:0.01928:1.41661:60:291:0.5629:0.007:0.1 0/1:1114:288:140,147:273,303:576,288:0.2585:2,2:49.1:1:34.7:1:0.71802:1.06:60:143:0.5089:0:0.1
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chr17 41267519 41267519 A - intronic BRCA1 . . . rs35149296 . 259610 Breast-ovarian_cancer,_familial_1|not_provided MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MedGen:CN517202 reviewed_by_expert_panel Benign 0.427117 0.4544 . . . . . . . . . 0.3691 0.2719 0.4219 0.4183 0.4098 0.4723 0.4013 0.4397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 286 789 chr17 41267518 . CA C 286 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=708;VD=265;AF=0.3743;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.46737;SOR=0.98562;LSEQ=GACAGAGCGAGACTTTGTCT;RSEQ=AAAAAAAAAAAAAAGATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:265:174,91:197,109:306,265:0.3743:2,2:40.3:1:34.9:1:0.79205:1.06:60:530:0.3754:0.0381:0.2 0/1:789:298:205,93:219,97:316,298:0.3777:2,2:39.7:1:34.8:1:0.93046:1.02421:60:596:0.3782:0.0507:0.1
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chr17 41275367 41275373 TTTTTTT - intronic BRCA1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 251 597 chr17 41275366 . GTTTTTTT G 251 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=601;VD=111;AF=0.1847;SHIFT3=18;MSI=25.000;MSILEN=1;SSF=0.00173;SOR=0.65762;LSEQ=CAACGACACCGATCATCCAT;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:111:52,59:90,109:199,111:0.1847:2,2:51:1:34.7:1:0.8127:1.07:60:222:0.1866:0.005:0.2 0/1:597:153:77,76:109,95:204,153:0.2563:2,2:44.4:1:34.6:1:0.59325:1.13207:60:306:0.2602:0.0335:0.2
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chr17 41277187 41277187 G C intronic BRCA1 . . . rs799905 ID=COSV58786469;OCCURENCE=1(large_intestine),1(biliary_tract),2(haematopoietic_and_lymphoid_tissue),2(upper_aerodigestive_tract) 186980 Breast-ovarian_cancer,_familial_1|not_specified|not_provided MONDO:MONDO:0011450,MedGen:C2676676,OMIM:604370|MedGen:CN169374|MedGen:CN517202 reviewed_by_expert_panel Benign 0.545128 0.371 . 0.4808 0.7766 0.4565 0.4453 0.5 0.3792 0.4407 0.5116 0.4941 0.8108 0.3697 0.3357 0.3759 0.4027 0.3576 0.4045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q21.31 0.5 320 1334 chr17 41277187 . G C 320 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1459;VD=669;AF=0.4585;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00614;SOR=1.21453;LSEQ=AGGTTCCGCCCCTACCCCCC;RSEQ=TCAAAGAATACCCATCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1459:669:392,277:430,354:784,669:0.4585:2,2:39.8:1:34.2:1:0.15219:1.16:60:54.75:0.4859:0.0171:1.2 0/1:1334:548:298,250:417,329:746,548:0.4108:2,2:40.3:1:34.1:1:0.61074:1.06326:60:44.667:0.4278:0:1.2
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chr17 56769979 56769979 C T intron RAD51C NM_002876:c.-26C>T;NM_058216:c.-26C>T . . rs12946397 ID=COSV53625930;OCCURENCE=1(lung) 345189 Fanconi_anemia|not_specified|Breast_and_Ovarian_Cancer_Susceptibility|not_provided MONDO:MONDO:0019391,MeSH:D005199,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374|MedGen:CN239207|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.158347 0.1766 0.1780 0.1771 0.1417 0.1107 0.1753 0.2531 0.1999 0.1545 0.1378 0.1954 0.1372 0.1444 0.0695 0.1652 0.2559 0.2232 0.2070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 335 1758 chr17 56769979 . C T 335 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1719;VD=853;AF=0.4962;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03669;SOR=1.13185;LSEQ=GGGCGTGCGGAGTTTGGCTG;RSEQ=TCCGGGGTTAGCAGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1719:853:636,217:632,230:862,853:0.4962:2,2:37.2:1:34.5:1:0.58236:1.07:60:169.6:0.4988:0.0192:1.3 0/1:1758:818:608,210:676,258:934,818:0.4653:2,2:37.6:1:34.4:1:0.38659:1.10:60:203.5:0.4689:0.0137:1.3
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chr17 56771841 56771841 T - intronic RAD51C . . . rs35324884 . . . . . . . . . . . . . . . . . 0.1631 0.0688 0.1786 0.0957 0.1607 0.2362 0.2151 0.1850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 275 826 chr17 56771840 . AT A 275 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=854;VD=244;AF=0.2857;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.43411;SOR=1.02413;LSEQ=GAATACCTTTATTAAGCTGA;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:244:115,129:195,244:439,244:0.2857:2,2:46.8:1:34.8:1:0.52151:1.12:60:488:0.2871:0.0152:0.2 0/1:826:232:107,125:200,230:430,232:0.2809:2,2:46.5:1:34.9:1:0.93507:1.01583:60:464:0.2819:0.0133:0.2
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chr17 56772317 56772317 C G exonic RAD51C . synonymous SNV RAD51C:NM_002876:exon2:c.171C>G:p.A57A,RAD51C:NM_058216:exon2:c.171C>G:p.A57A rs780388449 . . . . . . . . . 9.447e-06 0 0 0 0 1.842e-05 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 327 1443 chr17 56772317 . C G 327 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1371;VD=666;AF=0.4858;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50004;SOR=0.99716;LSEQ=GGGATATCTAAAGCAGAAGC;RSEQ=TTAGAAACTCTGCAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1371:666:453,213:447,256:703,666:0.4858:2,2:35.2:1:34.5:1:0.08761:1.22:60:221:0.4893:0.0263:2 0/1:1443:702:481,221:493,242:735,702:0.4865:2,2:36.4:1:34.6:1:0.57259:1.07:60:174.5:0.4885:0.0208:2
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chr17 56772326 56772326 T G exonic RAD51C . synonymous SNV RAD51C:NM_002876:exon2:c.180T>G:p.T60T,RAD51C:NM_058216:exon2:c.180T>G:p.T60T rs755092293 . . . . . . . . . 9.434e-06 0 0 0 0 1.841e-05 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 325 1482 chr17 56772326 . T G 325 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1396;VD=676;AF=0.4842;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.3816;SOR=0.97505;LSEQ=AAAGCAGAAGCCTTAGAAAC;RSEQ=CTGCAAATTATCAGAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1396:676:460,216:447,265:712,676:0.4842:2,2:36.3:1:34:1:0.04225:1.26:60:47.286:0.4811:0.015:2 0/1:1482:727:497,230:505,246:751,727:0.4906:2,2:37.8:1:34.2:1:0.65633:1.05:60:44.438:0.4857:0.0128:2
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chr17 56774918 56774920 ACC CCA intronic RAD51C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 209 969 chr17 56774918 . ACC CCA 209 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Complex;DP=969;VD=66;AF=0.0668;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3226;SOR=1.10725;LSEQ=TCTTAAAAAAAAAAAAAAAA;RSEQ=AAAAAAAAAAACCACGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:66:41,25:518,302:820,66:0.0668:2,2:45.2:1:34.6:1:0.89484:1.0458:60:132:0.0737:0.0263:2.1 0/1:969:60:40,20:562,249:811,60:0.0614:2,2:45.4:1:34.4:1:0.66595:1.12835:60:59:0.0677:0.0133:2.1
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chr17 56774919 56774920 CC ACCA intronic RAD51C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 197 969 chr17 56774919 . CC ACCA 197 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Complex;DP=969;VD=50;AF=0.0516;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.27543;SOR=0.87057;LSEQ=CTTAAAAAAAAAAAAAAAAA;RSEQ=AAAAAAAAAAACCACGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:50:35,15:518,302:820,50:0.0516:2,2:47:1:32.8:1:0.36675:1.36:60:100:0.0559:0:0.1 0/1:969:57:39,18:562,249:811,57:0.0588:2,2:51.4:1:33.9:1:0.88273:1.04165:60:114:0.0654:0:0.1
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chr17 56774920 56774920 - A intronic RAD51C . . . rs547599226 . . . . . . 0.198882 0.0813 . . . . . . . . . 0.3003 0.1922 0.254 0.5 0.0748 0.3772 0.3769 0.3324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 275 965 chr17 56774920 . C CA 275 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=969;VD=209;AF=0.2157;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.01852;SOR=0.79516;LSEQ=TTAAAAAAAAAAAAAAAAAC;RSEQ=AAAAAAAAAAACCACGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:209:114,94:288,143:431,209:0.2157:2,2:43:1:34.9:1:0.00389:1.65935:60:418:0.5251:0:0.3 0/1:965:248:160,88:281,118:399,248:0.257:2,2:40.4:1:34.6:1:0.11925:1.30917:60:247:0.6449:0.0073:0.2
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chr17 56786454 56786454 T - intronic RAD51C . . . rs34570887 . . . . . . 0.455272 0.4732 . . . . . . . . . 0.2954 0.4477 0.1808 0.0841 0.4014 0.1201 0.2245 0.2459 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 266 608 chr17 56786453 . CT C 266 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=636;VD=200;AF=0.3145;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.06159;SOR=1.2212;LSEQ=TCCTTTTTCTTTTTGAATTA;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:200:99,101:140,112:252,200:0.3145:2,2:46.2:1:34.8:1:0.21797:1.27455:60:199:0.3139:0.0173:0.1 0/1:608:166:74,92:121,130:251,166:0.273:2,2:43.8:1:34.7:1:0.48415:1.15676:60:332:0.2735:0.0214:0.2
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chr17 56789759 56789759 - A intronic RAD51C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q22 0.5 144 900 chr17 56789759 . G GA 144 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=835;VD=15;AF=0.018;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44754;SOR=0.8964;LSEQ=TATGTATGCTTTTTGTAAAA;RSEQ=AAAAAAAAAGTTCTAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:835:15:13,2:533,244:777,15:0.018:2,2:33.9:1:34.3:1:0.16628:2.97:60:30:0.0215:0.0024:0.2 0/1:900:18:14,4:575,259:834,18:0.02:2,2:30.7:1:34.7:1:0.60695:1.58:60:36:0.0226:0.0033:0.1
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chr17 58743653 58743653 T - downstream PPM1D dist=13 . . rs879635863 . . . . . . . . . . . . . . . . . 0.0074 0.0074 0.0235 0.0152 0 0.0367 0.0035 0.0152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 251 1146 chr17 58743652 . AT A 251 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1124;VD=138;AF=0.1228;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.37009;SOR=0.95115;LSEQ=CACTAACAAAGTTGAGAATA;RSEQ=TTTTTTTTTTTTTAACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1124:138:51,87:429,537:966,138:0.1228:2,2:40.9:1:35:1:0.11841:1.36242:60:276:0.1232:0.0071:0.2 0/1:1146:147:71,76:414,552:966,147:0.1283:2,2:43.1:1:34.9:1:0.24576:1.25:60:294:0.1285:0.0061:0.1
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chr17 59760996 59760996 A G exonic BRIP1 . synonymous SNV BRIP1:NM_032043:exon20:c.3411T>C:p.Y1137Y rs4986763 ID=COSV51995377;OCCURENCE=1(stomach),1(large_intestine) 185195 Neoplasm_of_ovary|Fanconi_anemia,_complementation_group_J|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|MONDO:MONDO:0012187,MedGen:C1836860,OMIM:609054|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.620807 0.754 0.6060 0.5932 0.6551 0.8026 0.7238 0.4284 0.5839 0.5620 0.4527 0.5824 0.6486 0.7584 0.6291 0.7076 0.4205 0.5619 0.5133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 1 376 1955 chr17 59760996 . A G 376 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1937;VD=1926;AF=0.9943;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31608;SOR=0.71949;LSEQ=TCATCTGTATCTTCAGGATC;RSEQ=TAAAGTTCAGGTGTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1937:1926:1110,816:2,1:3,1926:0.9943:2,2:36:1:34.4:1:1:1.46999:60:82.739:0.9958:0.0609:1.1 1/1:1955:1947:1140,807:2,0:2,1947:0.9959:0,2:36.3:1:34.5:1:0.51452:0:60:101.474:0.9974:0.0583:1.1
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chr17 59763114 59763114 A T intronic BRIP1 . . . rs4988357 ID=COSV51997887;OCCURENCE=1(upper_aerodigestive_tract),4(large_intestine) 1265721 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_single_submitter Benign 0.343051 0.5089 . 0.3938 0.4109 0.2867 0.5701 0.2894 0.4238 0.3707 0.3229 0.3350 0.3516 0.2392 0.3444 0.5093 0.2521 0.3356 0.2653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 324 1315 chr17 59763114 . A T 324 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1260;VD=635;AF=0.504;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06767;SOR=1.12847;LSEQ=ACCACCATATTTAAGGAATT;RSEQ=ATCTATACCCAAATAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1260:635:458,177:431,193:624,635:0.504:2,2:38.2:1:34.9:1:0.24029:1.16:60:1270:0.5044:0.0135:1.1 0/1:1315:623:434,189:488,204:692,623:0.4738:2,2:38.2:1:35:1:0.76301:1.04174:60:1246:0.4738:0.0175:1.1
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chr17 59763347 59763347 A G exonic BRIP1 . nonsynonymous SNV BRIP1:NM_032043:exon19:c.2755T>C:p.S919P rs4986764 ID=COSV51995396;OCCURENCE=1(large_intestine),1(stomach) 137495 Neoplasm_of_ovary|Fanconi_anemia,_complementation_group_J|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|MONDO:MONDO:0012187,MedGen:C1836860,OMIM:609054|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.627796 0.755 0.6134 0.5963 0.6717 0.8078 0.7244 0.4282 0.5857 0.5620 0.4528 0.5893 0.6691 0.7655 0.6490 0.7063 0.4212 0.5632 0.5173 0.154 0.242 T 0.053 0.020 N 1 0.090 P . . . -0.86 0.754 T -0.7 0.199 N -0.937 0.432 T 0.000 0.000 T . . . . . 0.004 0.021 N c -1.143 -1.165 0.000 0.042 0.638 0.428 0 0.71 0.172 0.201 0.169 -1.189 0.016 0.001 0.137 0.000 0.016 5.650 0.168 . . . 17q23.2 1 366 2000 chr17 59763347 . A G 366 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1986;VD=1982;AF=0.998;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50433;SOR=1.24179;LSEQ=TGCTTCCAGTAAATAAGGTG;RSEQ=GGTACTGTACTTTAAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1986:1982:1175,807:1,0:1,1982:0.998:0,2:37:1:33.9:1:1:0:60:47.341:0.999:0.0493:1.3 1/1:2000:1995:1199,796:0,1:1,1995:0.9975:0,2:36.7:1:33.4:1:0.3993:0:60:31.705:0.9985:0.052:1.3
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chr17 59763465 59763465 T C exonic BRIP1 . synonymous SNV BRIP1:NM_032043:exon19:c.2637A>G:p.E879E rs4986765 . 185227 Neoplasm_of_ovary|Fanconi_anemia,_complementation_group_J|Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified|not_provided Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|MONDO:MONDO:0012187,MedGen:C1836860,OMIM:609054|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.815096 0.9127 0.7343 0.7214 0.9069 0.8775 0.8924 0.5210 0.6654 0.6974 0.6983 0.7178 0.9073 0.8473 0.7483 0.8812 0.5120 0.6355 0.6307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 1 383 2166 chr17 59763465 . T C 383 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2055;VD=2046;AF=0.9956;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18381;SOR=0.52607;LSEQ=TTGGAAAATTCAGCCAAGGA;RSEQ=TCCAGTGCACTTTCAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2055:2046:1057,989:0,1:1,2046:0.9956:0,2:37.7:1:34.5:1:0.48363:0:60:112.667:0.9971:0.0316:1.3 1/1:2166:2161:1209,952:1,1:2,2161:0.9977:2,2:37.4:1:34.6:1:1:1.27:60:165.231:0.9981:0.0452:1.3
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chr17 59792162 59792162 T - intronic BRIP1 . . . rs35246906 . . . . . . 0.434505 0.494 . . . . . . . . . 0.3227 0.3689 0.2366 0.3108 0.4445 0.2176 0.2999 0.2340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 273 928 chr17 59792161 . AT A 273 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=886;VD=201;AF=0.2269;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.09478;SOR=0.86047;LSEQ=CCTTCTTCAATGATTTGCTA;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:201:65,136:195,331:526,201:0.2269:2,2:46:1:34.9:1:0.26089:1.23228:60:402:0.2284:0.0192:0.6 0/1:928:236:84,152:211,298:509,236:0.2543:2,2:45:1:34.7:1:0.14719:1.28081:60:472:0.2551:0.0172:0.5
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chr17 59808441 59808441 A - intronic BRIP1 . . . rs762489777 ID=COSV51993436;OCCURENCE=9(biliary_tract) . . . . . . . . . . . . . . . . 0.0159 0.0047 0.0575 0.0603 0.0007 0.1875 0.0139 0.0266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 274 1160 chr17 59808440 . TA T 274 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1217;VD=224;AF=0.1841;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.16181;SOR=0.89752;LSEQ=TACTTTTGGCCAAACTATCT;RSEQ=AAAAAAAAAAAAAGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1217:224:115,109:517,398:915,224:0.1841:2,2:40.9:1:34.8:1:0.17711:1.23099:60:448:0.1841:0.014:0.1 0/1:1160:233:131,102:480,368:848,233:0.2009:2,2:41.6:1:34.9:1:0.94059:1.01559:60:466:0.2014:0.0172:0.2
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chr17 59808482 59808482 A - intronic BRIP1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.25 116 983 chr17 59808481 . GA G 116 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=1055;VD=8;AF=0.0076;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.3489;SOR=0.74357;LSEQ=GAAAAAAATACTCTGAGGAG;RSEQ=AAAAAAAGGTTTAAGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1055:8:5,3:511,536:1047,8:0.0076:2,2:45.1:1:35:0:0.49748:1.75:60:16:0.0076:0:0.1 0/1:983:10:6,4:458,515:973,10:0.0102:2,2:33.7:1:35:0:0.52981:1.69:60:20:0.0102:0:0.1
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chr17 59857599 59857599 - A intron BRIP1 NM_032043:exon13:c.1935+23->T . . rs776579803 ID=COSV51997637;OCCURENCE=2(meninges),1(biliary_tract) . . . . . . . 0.0557 0.1701 0.1424 0.1764 0.1193 0.0339 0.1457 0.2069 0.3265 0.0035 0.0012 0.0126 0.0171 0 0.0395 0.0019 0.0051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 256 1365 chr17 59857599 . C CA 256 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1394;VD=140;AF=0.1004;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.07019;SOR=0.82911;LSEQ=TAGAAACACTGAAGGCCTTC;RSEQ=AAAAAAAAAAACAACAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1394:140:94,45:644,296:940,140:0.1004:2,2:41.6:1:34.9:1:0.84532:1.04149:60:280:0.1502:0.0014:0.1 0/1:1365:162:106,55:674,302:976,162:0.1187:2,2:42.2:1:34.9:1:0.41104:1.15784:60:324:0.1675:0:0.1
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chr17 59857809 59857809 C G intron BRIP1 NM_032043:exon13:c.1795-47G>C . . rs4988351 ID=COSV51993354;OCCURENCE=1(stomach),20(soft_tissue),1(pancreas) 256299 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.789736 0.8026 0.7859 0.7455 0.8574 0.4729 0.8256 0.8045 0.7489 0.7625 0.7981 0.7917 0.8557 0.5421 0.7020 0.8430 0.8052 0.7641 0.7515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 301 928 chr17 59857809 . C G 301 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=865;VD=418;AF=0.4832;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10475;SOR=0.88421;LSEQ=AAAATTATCTTTAGAAGAGG;RSEQ=TGGGCAAAGTGGCTCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:865:418:148,270:147,294:441,418:0.4832:2,2:35.6:1:33.8:1:0.56532:1.10:60:40.8:0.4828:0.0185:1.1 1/0:928:477:163,314:148,301:449,477:0.514:2,2:37.7:1:33.9:1:0.72793:1.06:60:46.7:0.5126:0.0216:1.1
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chr17 59859299 59859299 T G intronic BRIP1 . . . rs7207212 . . . . . . 0.98762 1 . . . . . . . . . 0.9859 0.9572 1 1 0.9994 0.9905 0.9990 0.9965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 1 329 1114 chr17 59859299 . T G 329 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1227;VD=1223;AF=0.9967;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.44069;SOR=1.3783;LSEQ=CTCAAAAAAAAAAAAAAAAG;RSEQ=AAAATGTGATATTCTCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1227:1223:753,470:0,0:0,1223:0.9967:0,2:40.6:1:32.1:1:1:0:60:15.527:0.9983:0.0367:1.1 1/1:1114:1109:705,404:0,0:0,1109:0.9955:0,2:41.3:1:32.8:1:1:0:60:24.791:0.9991:0.0368:1.1
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chr17 59892476 59892476 A - intronic BRIP1 . . . rs11300875 . . . . . . 0.764577 0.7718 . . . . . . . . . 0.7817 0.8665 0.5086 0.6859 0.8394 0.6099 0.7490 0.7194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 304 1138 chr17 59892475 . GA G 304 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1173;VD=440;AF=0.3751;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.44988;SOR=1.01464;LSEQ=GAAAAATGCTAGAAGTGCTG;RSEQ=AAAAAAAAAAAAAACCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1173:440:272,168:366,248:614,440:0.3751:2,2:42:1:34.7:1:0.48262:1.10:60:439:0.3743:0.0367:0.7 0/1:1138:423:246,177:369,224:593,423:0.3717:2,2:43:1:34.8:1:0.1936:1.18506:60:846:0.3724:0.0343:0.7
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chr17 59892541 59892541 A G intronic BRIP1 . . . rs7222799 . . . . . . 0.807109 0.8036 . . . . . . . . . 0.8099 0.9012 0.5506 0.7020 0.8455 0.8255 0.7688 0.7578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 281 781 chr17 59892541 . A G 281 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=808;VD=383;AF=0.474;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07068;SOR=0.85846;LSEQ=TCCTCAGTTGTTTCATACCC;RSEQ=GCAGAATAGCTTTCATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:383:183,200:182,237:419,383:0.474:2,2:36.9:1:32.6:1:0.22798:1.19:60:24.533:0.467:0.0161:1.1 1/0:781:400:184,216:185,193:378,400:0.5122:2,2:37.3:1:32.6:1:0.42987:1.12508:60:21.222:0.504:0.0243:1.1
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chr17 59911032 59911032 A - intronic BRIP1 . . . . . . . . . . 0.353035 0.4415 . . . . . . . . . 0.4691 0.4580 0.5498 0.4466 0.7833 0.4 0.4356 0.4769 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 317 1544 chr17 59911031 . CA C 317 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1703;VD=554;AF=0.3253;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.15797;SOR=1.08178;LSEQ=GACAAAGCAAGACTCCACCT;RSEQ=AAAAAAAAAAAAAAAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1703:554:373,181:458,282:740,554:0.3253:2,2:39.6:1:34.8:1:0.04637:1.27:60:1108:0.3259:0.0435:0.2 0/1:1544:476:288,188:469,246:715,476:0.3083:2,2:40.4:1:34.9:1:0.07509:1.24428:60:952:0.3089:0.0466:0.1
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chr17 59926633 59926633 - A intron BRIP1 NM_032043:exon5:c.380-16->T . . rs545021924 ID=COSV52007537;OCCURENCE=1(oesophagus) 180955 Neoplasm_of_ovary|Fanconi_anemia,_complementation_group_J|Hereditary_cancer-predisposing_syndrome|not_specified Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|MONDO:MONDO:0012187,MedGen:C1836860,OMIM:609054|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.00159744 . 0.0011 0.0010 0 0.0004 0.0001 0 0.0004 0.0015 0.0045 0.0003 0.0001 0.0012 0 0.0012 0 0.0003 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.25 140 1189 chr17 59926633 . T TA 140 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1167;VD=16;AF=0.0137;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02318;SOR=2.73978;LSEQ=GGAGTCTTATATAAGTAATT;RSEQ=AAAAAAAACAGCATAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1167:16:6,10:511,588:1099,16:0.0137:2,2:45:1:35:1:0.61563:1.44794:60:32:0.0147:0.0009:0.1 0/0:1189:6:4,2:504,623:1127,6:0.005:2,2:55.7:1:35:0:0.41693:2.47:60:12:0.0053:0:0
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chr17 59941017 59941017 - A upstream BRIP1 dist=128 . . rs34753867 . 1276406 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign . . . . . . . . . . . 0.3492 0.5276 0.4258 0.2947 0.0418 0.3686 0.2651 0.3017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17q23.2 0.5 319 1667 chr17 59941017 . G GA 319 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1795;VD=567;AF=0.3159;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.1838;SOR=1.0715;LSEQ=GGCATCCAATGGAAGTCTCC;RSEQ=AAAAAAAAAAAAAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1795:567:344,223:334,247:581,567:0.3159:2,2:46.5:1:34.9:1:0.28039:1.14:60:1134:1:0:0.2 0/1:1667:502:289,212:335,220:555,502:0.3011:2,2:46:1:34.9:1:0.38104:1.1169:60:1004:0.9144:0:0.3
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chr18 673444 673449 TTAAAG - UTR3 ENOSF1;TYMS NM_001354068:c.*861_*856delCTTTAA;NM_001354067:c.*861_*856delCTTTAA;NM_001354066:c.*861_*856delCTTTAA;NM_001318760:c.*861_*856delCTTTAA;NM_001354065:c.*861_*856delCTTTAA;NM_202758:c.*861_*856delCTTTAA;NM_017512:c.*861_*856delCTTTAA;NM_001071:c.*447_*452delTTAAAG;NM_001354868:c.*447_*452delTTAAAG;NM_001354867:c.*447_*452delTTAAAG . . rs11280056 ID=COSV51891993;OCCURENCE=1(large_intestine),4(central_nervous_system) . . . . . 0.492013 0.6944 . . . . . . . . . 0.3854 0.5332 0.3401 0.3742 0.6977 0.2934 0.2937 0.3388 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18p11.32 0.5 327 1416 chr18 673443 . TTTAAAG T 327 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1452;VD=658;AF=0.4532;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.37597;SOR=0.97384;LSEQ=TGTAGAGTGTGGTTATGAAC;RSEQ=TTATAGTTGTTTTATATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1452:658:351,307:425,369:794,658:0.4532:2,2:40.5:1:35:1:0.95789:1.00738:60:1316:0.4535:0.0461:0.2 0/1:1416:651:334,317:385,379:764,651:0.4597:2,2:42.3:1:35:1:0.74904:1.04:60:1302:0.4607:0.0445:0.1
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chr18 48559556 48559556 - T intronic SMAD4 . . . rs34008927 ID=COSV61690945;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) . . . . . . . . . . . . . . . . 0.3150 0.2495 0.3075 0.4028 0.4631 0.1551 0.3434 0.2825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18q21.2 0.5 291 829 chr18 48559556 . A AT 291 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=975;VD=328;AF=0.3364;SHIFT3=21;MSI=22.000;MSILEN=1;SSF=0.4742;SOR=0.98866;LSEQ=TTACACCAGCATAACACAGC;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:975:328:146,182:145,97:242,328:0.3364:2,2:46.3:1:34.9:1:0.00036:1.8614:60:656:1:0.0092:0.2 0/1:829:281:147,133:142,98:240,281:0.339:2,2:49.6:1:34.7:1:0.13319:1.31028:60:139:1:0:0.2
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chr18 48577091 48577091 G A intronic SMAD4 . . . rs8084630 . . . . . . 0.373802 0.4583 . . . . . . . . . 0.3834 0.3921 0.3981 0.4371 0.4298 0.3979 0.3683 0.3808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18q21.2 1 375 1726 chr18 48577091 . G A 375 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1794;VD=1792;AF=0.9989;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.21079;SOR=2.60253;LSEQ=TGCTCTTGTTCTGGAGGGCA;RSEQ=TTAGTAGTAGTTTAGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1794:1792:953,839:0,1:1,1792:0.9989:0,2:39:1:34.7:1:0.46849:0:60:148.333:1:0.0412:1.1 1/1:1726:1721:924,797:0,0:0,1721:0.9971:0,2:40.9:1:34.6:1:1:0:60:121.929:0.9982:0.0075:1.1
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chr18 48577782 48577782 G C intronic SMAD4 . . . rs7229678 ID=COSV61690958;OCCURENCE=1(breast),6(meninges),1(haematopoietic_and_lymphoid_tissue) . . . . . 0.376398 0.4583 . 0.2973 0.3989 0.3333 0.5469 . 0.3794 0.3390 0.2601 0.3848 0.4051 0.3902 0.4067 0.4288 0.3970 0.3650 0.3793 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18q21.2 1 347 1100 chr18 48577782 . G C 347 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1176;VD=1172;AF=0.9966;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16255;SOR=2.14581;LSEQ=GACAAAGGAATGATACAAGA;RSEQ=CAGGTAACTAAAAGTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1176:1172:584,588:0,1:1,1172:0.9966:0,2:41.9:1:34.1:1:1:0:60:52.273:0.9991:0.0196:1.1 1/1:1100:1092:538,554:0,1:1,1092:0.9927:0,2:42.8:1:34:1:1:0:60:59.667:0.9944:0.0173:1.1
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chr18 48584855 48584855 - TT intron SMAD4 NM_005359:exon7:c.904+29->TT . . rs386387676 . 1215968 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.0117812 0.0198 . 0.1520 0.0971 0.1581 0.1888 0.1877 0.1595 0.1586 0.1214 0.3070 0.2009 0.3304 0.395 0.3952 0.2886 0.3583 0.2978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18q21.2 0.5 300 936 chr18 48584855 . A ATT 300 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=977;VD=397;AF=0.4063;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.43648;SOR=1.01944;LSEQ=TTGTTTTTGTTGTAAGGGCT;RSEQ=TTTTTTTTTTTTTTTTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:977:397:160,236:68,90:158,397:0.4063:2,2:47.4:1:34.8:1:0.568:1.11422:60:396:1:0:0.2 0/1:936:376:150,225:81,95:176,376:0.4017:2,2:48.6:1:34.6:1:0.19539:1.27835:60:124:1:0:0.2
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chr19 1220728 1220728 - C intron STK11 NM_000455:exon5:c.734+12->C . . rs730881962 . 181069 Peutz-Jeghers_syndrome|Hereditary_cancer-predisposing_syndrome|not_specified MONDO:MONDO:0008280,MeSH:D010580,MedGen:C0031269,OMIM:175200,Orphanet:ORPHA2869,SNOMED_CT:54411001|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374 criteria_provided,_conflicting_interpretations Conflicting_interpretations_of_pathogenicity . . 0.0017 3.045e-05 0 0 0 0 5.839e-05 0 0 6.485e-05 0 0 0 0 0 0.0001 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.3 0.25 160 2260 chr19 1220728 . G GC 160 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=2209;VD=24;AF=0.0109;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00131;SOR=3.53472;LSEQ=GGTCACCCTGTAAGTGCCCC;RSEQ=CCCCCCCGGGCACTCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2209:24:10,14:902,1184:2086,24:0.0109:2,2:42.2:1:35:1:1:1.06654:60:48:0.0117:0.0005:0.2 0/0:2260:7:4,3:961,1196:2157,7:0.0031:2,2:47.1:1:33.4:1:0.70703:1.66:60:14:0.0033:0:0.4
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chr19 3113305 3113305 G C intron GNA11 NM_002067:exon3:c.322-23G>C . . rs1682811 ID=COSV99312883;OCCURENCE=2(central_nervous_system) 1272829 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.835663 0.7659 0.8749 0.8486 0.9046 0.9180 0.7689 0.8735 0.8678 0.8314 0.7352 0.8744 0.9104 0.9057 0.8411 0.7426 0.8728 0.8658 0.8912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.3 1 378 1966 chr19 3113305 . G C 378 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1846;VD=1840;AF=0.9967;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45741;SOR=0.78197;LSEQ=GGCCCCAGCGAGCTCTCGAC;RSEQ=TCTCCCCTGCCCGCCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1846:1840:1227,613:0,0:0,1840:0.9967:0,2:41.4:1:34.7:1:1:0:60:229:0.9984:0.0033:1.2 1/1:1966:1961:1373,588:0,0:0,1961:0.9975:0,2:39.8:1:34.6:1:1:0:60:177.273:0.9985:0.0371:1.2
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chr19 3115124 3115124 C T intronic GNA11 . . . rs10407783 ID=COSV50141885;OCCURENCE=2(central_nervous_system),1(lung) 1165122 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.183107 0.1746 . . . . . . . . . 0.2480 0.1148 0.1722 0.3543 0.2126 0.3515 0.3025 0.3139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.3 1 370 1659 chr19 3115124 . C T 370 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1649;VD=1637;AF=0.9927;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49413;SOR=0.91058;LSEQ=CACTGAGAGGCTCATTTGCC;RSEQ=GGTGTGCCGGCTCATGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1649:1637:641,996:1,2:3,1637:0.9927:2,2:42.1:1:34.7:1:1:1.29:60:271.833:0.9963:0.0115:1.2 1/1:1659:1648:657,991:0,0:0,1648:0.9934:0,2:39.5:1:34.7:1:1:0:60:548.333:0.9964:0.0428:1.1
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chr19 3119184 3119184 T G intron GNA11 NM_002067:exon6:c.736-20T>G . . rs308046 ID=COSV99312888;OCCURENCE=2(central_nervous_system) 256850 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.773562 0.7659 0.8159 0.8324 0.7258 0.9101 0.7683 0.8727 0.8678 0.8275 0.7350 0.8281 0.7489 0.8914 0.8411 0.7451 0.8723 0.8656 0.8801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.3 1 384 2351 chr19 3119184 . T G 384 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2429;VD=2408;AF=0.9914;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.34968;SOR=0.83522;LSEQ=GGAGGGCCCCTCTGATTCCC;RSEQ=CTGCCTTCGCTCCCGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2429:2408:1425,983:1,0:1,2408:0.9914:0,2:38.8:1:34.2:1:1:0:60:67.8:0.9937:0.056:1.1 1/1:2351:2334:1325,1009:0,0:0,2334:0.9928:0,2:38.1:1:34.3:1:1:0:60:110.143:0.997:0.0485:1.1
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chr19 17937758 17937758 C T intron JAK3 NM_000215:exon24:c.3208-39G>A . . rs3212798 ID=COSV101512982;OCCURENCE=1(meninges) 1280677 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.20607 0.0149 0.2592 0.1697 0.4238 0.0982 0.0171 0.1518 0.1767 0.1834 0.1409 0.2270 0.4192 0.1196 0.2020 0.0130 0.1393 0.1699 0.1568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.11 0.5 331 1498 chr19 17937758 . C T 331 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1524;VD=773;AF=0.5072;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30602;SOR=1.04036;LSEQ=ATAATGGGGTCGTGCCTGAG;RSEQ=AGTCCAAAGGACACAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1524:773:320,453:310,438:748,773:0.5072:2,2:42.9:1:34.6:1:1:1.00193:60:153.6:0.5076:0.0151:1.2 0/1:1498:745:300,445:310,441:751,745:0.4973:2,2:43.1:1:34.7:1:0.71275:1.0427:60:185.25:0.4983:0.02:1.1
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chr19 17942005 17942005 A G intron JAK3 NM_000215:exon21:c.2978+32T>C . . rs3212774 ID=COSV71685378;OCCURENCE=2(central_nervous_system),11(soft_tissue),1(lung) 1232732 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.433706 0.4722 0.3501 0.3820 0.4191 0.5355 0.4501 0.3487 0.3279 0.3416 0.4188 0.3528 0.3936 0.4663 0.25 0.4556 0.3330 0.3176 0.3712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.11 0.5 338 1755 chr19 17942005 . A G 338 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1834;VD=897;AF=0.4891;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48117;SOR=1.0054;LSEQ=CGGAGCCAGAGCCGTGGGGA;RSEQ=TAGGGGCGGAGCCTAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1834:897:702,195:719,216:935,897:0.4891:2,2:39:1:34.5:1:0.50166:1.08:60:223.25:0.4909:0.0098:1.4 0/1:1755:856:693,163:723,174:897,856:0.4877:2,2:39.1:1:34.2:1:0.85591:1.02:60:70.333:0.4884:0.0137:1.5
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chr19 17952185 17952185 G T intron JAK3 NM_000215:exon8:c.1142+13C>A . . rs3212733 ID=COSV71685726;OCCURENCE=6(meninges),7(soft_tissue) 141304 Severe_combined_immunodeficiency,_autosomal_recessive,_T_cell-negative,_B_cell-positive,_NK_cell-negative|not_specified MONDO:MONDO:0010938,MedGen:C1833275,OMIM:600802,Orphanet:ORPHA35078|MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.113818 0.0486 0.1190 0.1568 0.0507 0.2922 0.0685 0.28 0.2200 0.1393 0.1387 0.1317 0.0352 0.2279 0.1987 0.0370 0.1700 0.1789 0.1885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.11 0.5 340 1972 chr19 17952185 . G T 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1943;VD=923;AF=0.475;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02078;SOR=0.87603;LSEQ=CACAGAGGCCGGGAATGGGG;RSEQ=ACAGGTCCTTACGTGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1943:923:674,249:709,307:1016,923:0.475:2,2:38.3:1:34.4:1:0.11929:1.17:60:114.375:0.4761:0.0206:1.1 1/0:1972:1002:730,272:690,275:965,1002:0.5081:2,2:38.8:1:34.2:1:0.5132:1.07:60:90.091:0.5116:0.0223:1.1
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chr19 17952609 17952609 T G intron JAK3 NM_000215:exon7:c.862-38A>C . . rs3212730 ID=COSV71685727;OCCURENCE=7(meninges),9(soft_tissue),1(upper_aerodigestive_tract) 1255321 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.194888 0.1796 0.1844 0.2326 0.1059 0.3447 0.1963 0.2185 0.2341 0.2301 0.2345 0.1997 0.1091 0.2971 0.3067 0.1975 0.2190 0.2369 0.2541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.11 0.5 332 1840 chr19 17952609 . T G 332 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1918;VD=862;AF=0.4494;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04099;SOR=0.89052;LSEQ=TACCGAAGTGGGGGCCCAGC;RSEQ=GGACCCCGCCAAACCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1918:862:313,549:367,678:1045,862:0.4494:2,2:40:1:34.5:1:0.59751:1.05:60:214.5:0.4516:0.0141:1.2 0/1:1840:880:280,600:325,624:949,880:0.4783:2,2:40.1:1:34:1:0.2743:1.116:60:61.857:0.479:0.0152:1.1
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chr19 17955021 17955021 G A intron JAK3 NM_000215:exon2:c.184+22C>T . . rs3212711 ID=COSV71685729;OCCURENCE=11(meninges),2(central_nervous_system),10(soft_tissue) 1173205 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.406749 0.3641 0.3619 0.4153 0.5608 0.4971 0.4545 0.3824 0.4086 0.3585 0.3541 0.3436 0.4980 0.3282 0.3709 0.3312 0.2249 0.2847 0.3147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.11 0.5 317 1373 chr19 17955021 . G A 317 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1410;VD=559;AF=0.3965;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45807;SOR=0.98891;LSEQ=CCCATCCTTCCCTCTGGCCC;RSEQ=ATCCACTAGGGATGCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1410:559:307,252:517,330:847,559:0.3965:2,2:33.6:1:34.8:1:0.02342:1.28574:60:278.5:0.4004:0.0184:2.4 0/1:1373:548:287,261:503,321:824,548:0.3991:2,2:37.5:1:34.9:1:0.00149:1.42461:60:1096:0.4023:0:2.5
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chr19 17955112 17955112 G - exonic JAK3 . frameshift deletion JAK3:NM_000215:exon2:c.115delC:p.Q39Sfs*108 . ID=COSV71685743;OCCURENCE=2(large_intestine),3(stomach),1(skin),1(thyroid),1(endometrium) 647819 Severe_combined_immunodeficiency,_autosomal_recessive,_T_cell-negative,_B_cell-positive,_NK_cell-negative|not_provided MONDO:MONDO:0010938,MedGen:C1833275,OMIM:600802,Orphanet:ORPHA35078|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Pathogenic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19p13.11 0.25 157 2280 chr19 17955111 . TG T 157 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Deletion;DP=2347;VD=11;AF=0.0047;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.02328;SOR=0.46216;LSEQ=CAAAGGAGAAAGATAGGCGC;RSEQ=GGGGGGCCCGGGGCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2347:11:7,4:1316,1019:2335,11:0.0047:2,2:35.8:1:35:1:0.76515:1.35:60:22:0.0047:0.0009:0.1 0/1:2280:23:12,11:1281,976:2257,23:0.0101:2,2:30.3:1:34.9:1:0.67733:1.20302:60:46:0.0101:0.0022:0.4
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chr19 44055726 44055726 T C exonic XRCC1 . nonsynonymous SNV XRCC1:NM_006297:exon10:c.1196A>G:p.Q399R rs25487 ID=COSV53447249;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue) 227806 Platinum_compounds_response_-_Efficacy|not_provided .|MedGen:CN517202 reviewed_by_expert_panel drug_response 0.739617 0.7649 0.7092 0.6853 0.8588 0.7500 0.7430 0.6836 0.6458 0.6638 0.6499 0.7200 0.8520 0.7231 0.5960 0.7370 0.7022 0.6510 0.6691 1.0 0.010 T 0.000 0.537 N 0.999 0.216 P . . . 2.81 0.110 T 2.1 0.004 N -0.976 0.358 T 0.000 0.000 T . . . . . 0.408 0.263 N c -0.600 -0.452 0.319 0.194 0.707 0.730 0 4.13 0.475 1.982 0.400 0.069 0.176 1.000 0.715 0.976 0.476 7.732 0.278 BRCT domain ENSG00000176472.6|ENSG00000176472.6|ENSG00000176472.6|ENSG00000176472.6|ENSG00000176531.6|ENSG00000176472.6|ENSG00000176472.6|ENSG00000124466.8|ENSG00000176472.6|ENSG00000176472.6|ENSG00000073050.7|ENSG00000073050.7|ENSG00000124466.8|ENSG00000176472.6|ENSG00000234465.6|ENSG00000176472.6|ENSG00000073050.7|ENSG00000176472.6 Adipose_Subcutaneous|Adipose_Visceral_Omentum|Artery_Aorta|Artery_Tibial|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Esophagus_Mucosa|Lung|Nerve_Tibial|Nerve_Tibial|Pancreas|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Stomach|Testis|Thyroid 19q13.31 0.5 336 1974 chr19 44055726 . T C 336 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1969;VD=978;AF=0.4967;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50657;SOR=1.00098;LSEQ=GGCGTGTGAGGCCTTACCTC;RSEQ=GGGAGGGCAGCCGCCGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1969:978:508,470:519,470:989,978:0.4967:2,2:40:1:33.3:1:0.82154:1.02165:60:27.765:0.4906:0.0081:1.2 0/1:1974:980:487,493:497,493:990,980:0.4965:2,2:39.3:1:33.9:1:0.82192:1.02053:60:39.833:0.4933:0.0117:1.1
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chr19 45854919 45854919 T G exonic ERCC2 . nonsynonymous SNV ERCC2:NM_000400:exon23:c.2251A>C:p.K751Q rs13181 ID=COSV67266431;OCCURENCE=14(soft_tissue),1(skin),1(thyroid) 137844 Non-small_cell_lung_carcinoma|Bone_osteosarcoma|Xeroderma_pigmentosum,_group_D|Trichothiodystrophy_1,_photosensitive|Cerebrooculofacioskeletal_syndrome_2|not_specified|not_provided Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|MONDO:MONDO:0002629,MeSH:D012516,MedGen:C0585442,OMIM:259500,Orphanet:ORPHA668|MONDO:MONDO:0010212,MedGen:C0268138,OMIM:278730,SNOMED_CT:68637004|MONDO:MONDO:0011125,MedGen:C1866504,OMIM:601675,Orphanet:ORPHA670|MONDO:MONDO:0012553,MedGen:C1853102,OMIM:610756|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign/Likely_benign 0.236621 0.0764 0.3260 0.3269 0.2217 0.1852 0.0759 0.4133 0.3854 0.3112 0.3737 0.3203 0.2284 0.2273 0.4172 0.0749 0.4037 0.3817 0.3579 0.582 0.059 T 0.200 0.166 N 1 0.090 P -0.165 0.043 N -1.42 0.825 T -0.94 0.251 N -1.087 0.061 T 0.000 0.000 T . . . . . 0.024 0.067 N c -0.788 -0.643 0.833 0.247 0.707 0.730 0 4.29 0.502 1.271 0.325 0.127 0.214 0.995 0.385 0.068 0.175 11.392 0.489 . ENSG00000104884.10|ENSG00000104884.10|ENSG00000117877.6|ENSG00000104892.12|ENSG00000104884.10|ENSG00000104884.10|ENSG00000104884.10|ENSG00000117877.6|ENSG00000007047.10|ENSG00000104884.10|ENSG00000117877.6|ENSG00000104884.10|ENSG00000117877.6|ENSG00000012061.11|ENSG00000104884.10|ENSG00000104884.10|ENSG00000104892.12|ENSG00000104884.10|ENSG00000104892.12|ENSG00000104884.10|ENSG00000104884.10|ENSG00000104884.10 Adipose_Subcutaneous|Artery_Aorta|Breast_Mammary_Tissue|Esophagus_Mucosa|Esophagus_Mucosa|Heart_Atrial_Appendage|Heart_Left_Ventricle|Heart_Left_Ventricle|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Testis|Thyroid 19q13.32 0.5 357 2575 chr19 45854919 . T G 357 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2633;VD=1333;AF=0.5063;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42611;SOR=1.01193;LSEQ=AGCAATCTGCTCTATCCTCT;RSEQ=CAGCGTCTCCTCTGATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2633:1333:704,629:671,622:1293,1333:0.5063:2,2:38.9:1:34.4:1:0.63936:1.04:60:101.538:0.505:0.0197:1.2 1/0:2575:1296:699,597:663,607:1270,1296:0.5033:2,2:39.4:1:34.6:1:0.38438:1.07:60:128.6:0.5025:0.0179:1.2
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chr19 45867216 45867216 - G intron ERCC2 NM_000400:exon10:c.949+28->C;NM_000400:exon11:c.950-47->C;NM_001130867:exon9:c.877+28->C;NM_001130867:exon10:c.878-47->C . . rs766117419 ID=COSV99059896;OCCURENCE=1(skin) 257146 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.438099 0.4405 0.3478 0.2783 0.7618 0.2876 0.5157 0.25 0.2301 0.3115 0.2497 0.3661 0.7490 0.2955 0.23 0.4560 0.1989 0.1879 0.2454 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.32 0.5 310 1129 chr19 45867216 . T TG 310 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1105;VD=483;AF=0.4371;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20583;SOR=0.92914;LSEQ=CGGGGAGGCGGGAAAGGGAC;RSEQ=GGGGGGCAGCGGGGGGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1105:483:380,103:445,109:554,483:0.4371:2,2:44.6:1:34.4:1:0.53724:1.10648:60:482:0.9488:0:0.3 0/1:1129:514:383,131:427,135:562,514:0.4553:2,2:44.4:1:34.5:1:0.62054:1.08177:60:256:1:0.0053:0.4
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chr19 45867223 45867227 CAGCG GCAGC splicing ERCC2 NM_000400:exon10:r.spl;NM_001130867:exon9:r.spl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.32 0.25 123 1212 chr19 45867223 . CAGCG GCAGC 123 PASS STATUS=StrongSomatic;SAMPLE=NCCL202312;TYPE=Complex;DP=1172;VD=15;AF=0.0128;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00002;SOR=0;LSEQ=GCGGGAAAGGGACTGGGGGG;RSEQ=GGGGGTCGGGGCTCACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1172:15:9,6:860,293:1153,15:0.0128:2,2:32.8:1:31.5:1:0.23219:1.95558:60:30:0.0129:0.0051:0.5 0/0:1212:0:0,0:856,351:1207,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0
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chr19 45912734 45912736 AGC - exonic CD3EAP . nonframeshift deletion CD3EAP:NM_001297590:exon3:c.1514_1516del:p.Q510del,CD3EAP:NM_012099:exon3:c.1508_1510del:p.Q508del rs775597312 ID=COSV99185425;OCCURENCE=1(stomach) . . . . . . . . 0.0001 0.0003 0.0001 0 0 0.0002 0 6.777e-05 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.32 0.5 180 1864 chr19 45912733 . AAGC A 180 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1845;VD=37;AF=0.0201;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.29849;SOR=1.17155;LSEQ=CAGGCCGGGACAAGAAGCGG;RSEQ=AGCAGCAGCAGCAGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1845:37:24,13:1056,749:1805,37:0.0201:2,2:44.5:1:34.7:1:0.50216:1.31:60:74:0.0201:0.0011:0.2 0/1:1864:32:18,14:1112,719:1831,32:0.0172:2,2:40.1:1:35:1:0.59058:1.20278:60:64:0.0173:0.0016:0.2
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chr19 45923653 45923653 A G exonic ERCC1 . synonymous SNV ERCC1:NM_001369411:exon3:c.354T>C:p.N118N,ERCC1:NM_001369416:exon3:c.354T>C:p.N118N,ERCC1:NM_001369419:exon3:c.354T>C:p.N118N,ERCC1:NM_202001:exon3:c.354T>C:p.N118N,ERCC1:NM_001166049:exon4:c.354T>C:p.N118N,ERCC1:NM_001369408:exon4:c.354T>C:p.N118N,ERCC1:NM_001369409:exon4:c.354T>C:p.N118N,ERCC1:NM_001369410:exon4:c.354T>C:p.N118N,ERCC1:NM_001369412:exon4:c.354T>C:p.N118N,ERCC1:NM_001369415:exon4:c.354T>C:p.N118N,ERCC1:NM_001369418:exon4:c.354T>C:p.N118N,ERCC1:NM_001983:exon4:c.354T>C:p.N118N,ERCC1:NM_001369413:exon5:c.354T>C:p.N118N,ERCC1:NM_001369414:exon5:c.354T>C:p.N118N,ERCC1:NM_001369417:exon5:c.354T>C:p.N118N rs11615 . 227808 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.66893 0.7381 0.5401 0.5159 0.8915 0.7316 0.7385 0.3724 0.3843 0.4637 0.5391 0.5425 0.875 0.6691 0.4338 0.7413 0.3622 0.3723 0.4187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.32 0.5 355 2327 chr19 45923653 . A G 355 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2514;VD=1256;AF=0.4996;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00938;SOR=1.1468;LSEQ=TCGCCAAATTCCCAGGGCAC;RSEQ=TTGCGCACGAACTTCAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2514:1256:682,574:725,529:1254,1256:0.4996:2,2:40:1:34.5:1:0.07697:1.15341:60:138.556:0.4984:0.0119:1.1 0/1:2327:1083:582,501:624,608:1232,1083:0.4654:2,2:39.4:1:34.3:1:0.14455:1.13:60:97.455:0.4651:0.0185:1.1
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chr19 50909389 50909389 T G intron POLD1 NM_001256849:exon11:c.1243-50T>G;NM_002691:exon11:c.1243-50T>G;NM_001308632:exon10:c.1243-50T>G . . rs1673041 ID=COSV70955475;OCCURENCE=3(lung) 670373 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 0.704473 0.3075 0.8109 0.7341 0.9059 0.8406 0.2786 0.7486 0.7562 0.7278 0.7031 0.7746 0.9017 0.8182 0.6678 0.2944 0.7319 0.7635 0.75 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.33 0.5 343 1887 chr19 50909389 . T G 343 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1896;VD=970;AF=0.5116;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16897;SOR=1.06654;LSEQ=CAATCTCCGTTCTTCAGGCT;RSEQ=ATGTGACGGGGACCCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1896:970:646,324:628,297:925,970:0.5116:2,2:37.6:1:34.6:1:0.55718:1.06045:60:193:0.5111:0.0174:1.1 0/1:1887:935:617,318:626,322:948,935:0.4955:2,2:38.2:1:34.6:1:1:1.00198:60:232.75:0.4949:0.018:1.1
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chr19 50911948 50911948 T - intron POLD1 NM_001308632:exon14:c.1776-16T>- . . rs752444586 ID=COSV70954460;OCCURENCE=1(liver),3(large_intestine),4(biliary_tract) 539399 Colorectal_cancer_10|not_provided MONDO:MONDO:0012953,MedGen:C2675481,OMIM:612591|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign . . . 0.2762 0.2880 0.2878 0.2917 0.1935 0.2698 0.2485 0.3264 0.0031 0.0045 0.0071 0.008 0 0.0107 0.0013 0.0038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.33 0.5 274 1949 chr19 50911947 . AT A 274 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1950;VD=202;AF=0.1036;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.07592;SOR=0.85949;LSEQ=CTGCTCCCAGCCAATGAATG;RSEQ=TTTTTTTTTTTAAAGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1950:202:125,77:1099,619:1718,202:0.1036:2,2:41.9:1:34.9:1:0.58826:1.09362:60:404:0.1038:0.0056:0.2 0/1:1949:231:161,70:1146,544:1690,231:0.1185:2,2:39.6:1:34.9:1:0.59893:1.09:60:462:0.1191:0.0123:0.2
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chr19 50911960 50911960 A T intron POLD1 NM_001308632:exon14:c.1776-4A>T . . . ID=COSV70955374;OCCURENCE=2(liver),1(pancreas) . . . . . . . . . . . . . . . . 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.33 0.5 189 2065 chr19 50911960 . A T 189 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=2125;VD=43;AF=0.0202;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41958;SOR=1.07292;LSEQ=ATGAATGATTTTTTTTTTTT;RSEQ=AAGGGTGAGGCCACAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2125:43:27,16:1300,767:2067,43:0.0202:2,2:40.1:1:35:0:1:1.00439:60:86:0.0203:0:1.1 0/1:2065:39:20,19:1334,686:2020,39:0.0189:2,2:44.6:1:34.7:1:0.06139:1.84686:60:78:0.0189:0:1.2
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chr19 50919797 50919797 C T intron POLD1 NM_001256849:exon23:c.2953+12C>T;NM_002691:exon23:c.2953+12C>T;NM_001308632:exon22:c.3031+12C>T . . rs3218776 ID=COSV54532142;OCCURENCE=1(oesophagus) 257197 Colorectal_cancer_10|Mandibular_hypoplasia,_deafness,_progeroid_features,_and_lipodystrophy_syndrome|not_specified|not_provided MONDO:MONDO:0012953,MedGen:C2675481,OMIM:612591|MONDO:MONDO:0014157,MedGen:C3715192,OMIM:615381,Orphanet:ORPHA363649|MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.408347 0.1429 0.5810 0.5688 0.4362 0.7358 0.2364 0.7623 0.6929 0.5658 0.4585 0.5601 0.3293 0.6938 0.5298 0.1361 0.6914 0.6986 0.6286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19q13.33 0.5 340 2618 chr19 50919797 . C T 340 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2667;VD=1242;AF=0.4657;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01068;SOR=0.87963;LSEQ=TGCTACTGCGTACGGGGGCA;RSEQ=CAGGGGACTGGGGGCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2667:1242:674,568:734,679:1413,1242:0.4657:2,2:38.4:1:32.6:1:0.24243:1.10:60:18.108:0.4564:0.0075:1.2 0/1:2618:1303:694,609:680,619:1299,1303:0.4977:2,2:39:1:32.9:1:0.66577:1.04:60:20.717:0.4905:0.0187:1.2
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chr20 36030939 36030939 G C exonic SRC . synonymous SNV SRC:NM_005417:exon12:c.1218G>C:p.A406A,SRC:NM_198291:exon12:c.1218G>C:p.A406A rs1885257 ID=COSV62440282;OCCURENCE=2(central_nervous_system),1(upper_aerodigestive_tract) . . . . . 1 1 . 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q11.23 1 396 2887 chr20 36030939 . G C 396 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2961;VD=2946;AF=0.9949;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52747;SOR=0.95704;LSEQ=AACCTGGTGTGCAAAGTGGC;RSEQ=GACTTTGGGCTGGCTCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2961:2946:1743,1203:0,0:0,2946:0.9949:0,2:36.4:1:34.4:1:1:0:60:88.273:0.9962:0.0618:1.1 1/1:2887:2873:1706,1167:2,1:3,2873:0.9952:2,2:37.8:1:34.4:1:1:1.36797:60:142.65:0.9979:0.0544:1.1
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chr20 36031097 36031097 A G intronic SRC . . . rs2145792 ID=COSV100658006;OCCURENCE=2(central_nervous_system) 1258158 not_provided MedGen:CN517202 criteria_provided,_single_submitter Benign 1 1 . . . . . . . . . 1 1 1 1 1 1 1 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q11.23 1 389 2629 chr20 36031097 . A G 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2445;VD=2437;AF=0.9967;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24019;SOR=1.51368;LSEQ=TTCCTCATGGTGCTTATCTA;RSEQ=CAGAGCGGTCATGACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2445:2437:1388,1049:1,1:2,2437:0.9967:2,2:37.8:1:34.4:1:1:1.32:60:100.542:0.9971:0.0671:1.1 1/1:2629:2616:1481,1135:2,2:4,2616:0.9951:2,2:37.9:1:34.3:1:1:1.30:60:108:0.9962:0.0582:1.1
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chr20 43961971 43961971 T C intronic SDC4 . . . rs6065805 . . . . . . 0.792732 0.9554 . . . . . . . . . 0.7608 0.7273 0.7924 0.7020 0.9617 0.7856 0.7538 0.7367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 376 1939 chr20 43961971 . T C 376 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1979;VD=1966;AF=0.9934;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4037;SOR=1.17898;LSEQ=AACCCTTGCTCTGCAAAGTG;RSEQ=GGATCCAAAAACCAATAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1979:1966:912,1054:2,3:5,1966:0.9934:2,2:40:1:34.4:1:1:1.30:60:102.474:0.9939:0.0515:2.3 1/1:1939:1924:853,1071:3,1:4,1924:0.9923:2,2:38.7:1:34.4:1:0.32861:3.76428:60:82.652:0.9937:0.0578:2.2
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chr20 43961997 43961997 T G intronic SDC4 . . . rs6073714 . . . . . . 0.789736 0.9554 . . . . . . . . . 0.7607 0.7273 0.7924 0.7020 0.9618 0.7860 0.7535 0.7363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 362 1455 chr20 43961997 . T G 362 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1521;VD=1513;AF=0.9947;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12777;SOR=0.39084;LSEQ=CAAAAACCAATAGCAACACC;RSEQ=GAGAGCTGGTTAGAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1521:1513:621,892:1,0:1,1513:0.9947:0,2:40.8:1:34.3:1:0.41083:0:60:107.071:0.9973:0.027:2.6 1/1:1455:1452:581,871:0,0:0,1452:0.9979:0,2:40.6:1:34.3:1:1:0:60:89.75:0.9986:0.0296:2.7
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chr20 43962593 43962596 AAAG - intronic SDC4 . . . . ID=COSV65595449;OCCURENCE=1(biliary_tract) . . . . . . . . . . . . . . . . 0.0003 0.0001 0.0022 0 0 0.0005 0.0003 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 0.5 218 1092 chr20 43962592 . AAAAG A 218 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1087;VD=76;AF=0.0699;SHIFT3=2;MSI=9.000;MSILEN=1;SSF=0.51176;SOR=0.99092;LSEQ=ATAATTCATTGGTTAAAAAA;RSEQ=AAGAAGAAATGTAGAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1087:76:37,39:535,472:1007,76:0.0699:2,2:41.7:1:35:1:0.47633:1.19454:60:152:0.0702:0.0028:0.2 0/1:1092:77:38,39:551,459:1010,77:0.0705:2,2:47:1:34.9:1:0.40721:1.23178:60:154:0.0709:0.0027:0.2
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chr20 43962594 43962596 AAG - intronic SDC4 . . . rs147893643 . . . . . . 0.494409 0.5139 . . . . . . . . . 0.4705 0.3713 0.6075 0.5101 0.5569 0.5007 0.5052 0.4746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 0.75 345 1134 chr20 43962593 . AAAG A 345 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=1113;VD=874;AF=0.7853;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.00693;SOR=0.76423;LSEQ=TAATTCATTGGTTAAAAAAA;RSEQ=AAGAAGAAATGTAGAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1113:874:472,402:82,82:164,874:0.7853:2,2:42.7:1:35:1:0.34959:1.17:60:1748:0.8428:0.0503:0.2 1/1:1134:938:499,439:74,45:119,938:0.8272:2,2:39.9:1:35:1:0.07842:1.44621:60:1876:0.8891:0.0891:0.2
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chr20 43962595 43962596 AG - intronic SDC4 . . . . . . . . . . . . . . . . . . . . . 0.0043 0.0146 0.0014 0 0 0 6.996e-05 0.0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 0.5 200 1080 chr20 43962594 . AAG A 200 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1074;VD=53;AF=0.0493;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0.16662;SOR=1.25174;LSEQ=AATTCATTGGTTAAAAAAAA;RSEQ=AAGAAGAAATGTAGAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1074:53:22,31:67,55:122,53:0.0493:2,2:37.5:1:35:1:0.13831:1.71115:60:106:0.3029:0.0047:0.1 0/1:1080:43:29,14:60,55:115,43:0.0398:2,2:43.1:1:35:0:0.10536:1.89:60:86:0.2722:0:0.1
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chr20 43962641 43962641 T - intronic SDC4 . . . rs35204147 . . . . . . 0.850839 0.9534 . . . . . . . . . 0.7725 0.8373 0.7476 0.6815 0.9489 0.6568 0.7347 0.7044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 0.5 320 849 chr20 43962640 . CT C 320 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=812;VD=535;AF=0.6589;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11357;SOR=0.87648;LSEQ=GCTGACTGAATCAAAATCTA;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:812:535:224,311:87,83:170,535:0.6589:2,2:44.1:1:34.9:1:0.04124:1.45449:60:1070:0.6597:0.0222:0.2 1/0:849:584:263,321:99,74:173,584:0.6879:2,2:42.7:1:34.9:1:0.00551:1.63177:60:1168:0.6887:0.0412:0.2
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chr20 43963047 43963047 C A intronic SDC4 . . . rs4812891 . . . . . . 0.850439 0.9554 . . . . . . . . . 0.8095 0.8973 0.7995 0.7020 0.9616 0.7858 0.7543 0.7474 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 385 2151 chr20 43963047 . C A 385 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2109;VD=2106;AF=0.9986;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51079;SOR=1.30779;LSEQ=GTGAGATGATGGATATATTA;RSEQ=TTAACTCCACTGTAGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2109:2106:1189,917:0,0:0,2106:0.9986:0,2:37.8:1:34.7:1:1:0:60:299.857:0.999:0.0531:1.1 1/1:2151:2147:1229,918:0,0:0,2147:0.9981:0,2:37.8:1:34.8:1:1:0:60:356.833:0.9981:0.053:1.1
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chr20 43963138 43963138 - T intronic SDC4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 0.25 133 1286 chr20 43963138 . A AT 133 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Insertion;DP=1288;VD=14;AF=0.0109;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05736;SOR=2.34371;LSEQ=AAATTTATTTTTTTATTTTT;RSEQ=TTTTTTTTCAAGACAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1288:14:6,8:525,691:1216,14:0.0109:2,2:45.3:1:35:0:1:1.01301:60:28:0.0116:0:1.2 0/0:1286:6:3,3:495,726:1221,6:0.0047:2,2:48.8:1:35:0:0.6915:1.47:60:12:0.0049:0:1.4
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chr20 43963437 43963437 T - intronic SDC4 . . . rs993199538 . . . . . . . . . . . . . . . . . 0.0028 0.0096 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 0.5 245 2028 chr20 43963436 . AT A 245 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Deletion;DP=2075;VD=128;AF=0.0617;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.45029;SOR=0.97586;LSEQ=CGTGCCCGGCCATAAAATTT;RSEQ=TTTTTTTTTAAACCAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2075:128:82,46:1260,684:1944,128:0.0617:2,2:43.7:1:35:1:0.84916:1.03339:60:256:0.0617:0.0043:1.4 0/1:2028:128:80,48:1237,653:1890,128:0.0631:2,2:42.4:1:35:1:0.50299:1.13652:60:256:0.0633:0.0049:1.3
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chr20 43963489 43963489 G C intronic SDC4 . . . rs6130811 . . . . . . 0.790335 0.9554 . . . . . . . . . 0.7586 0.7186 0.7919 0.7020 0.9617 0.7858 0.7544 0.7347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 387 2430 chr20 43963489 . G C 387 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2515;VD=2510;AF=0.998;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24074;SOR=0.41361;LSEQ=GTGCTTGGTAGGTGCCAAAA;RSEQ=CTTTAAGTCAGTTCAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2515:2510:1513,997:1,0:1,2510:0.998:0,2:35.9:1:34.3:1:1:0:60:75.061:0.9988:0.035:1.2 1/1:2430:2428:1427,1001:0,0:0,2428:0.9992:0,2:35.4:1:34.4:1:1:0:60:104.565:0.9992:0.0366:1.2
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chr20 43963735 43963735 A C intronic SDC4 . . . rs6104122 . . . . . . 0.790935 0.9554 . . . . . . . . . 0.7582 0.7183 0.7956 0.7061 0.9594 0.7874 0.7532 0.7310 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 365 1821 chr20 43963735 . A C 365 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=1793;VD=1778;AF=0.9916;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31908;SOR=1.24972;LSEQ=CCCGCCCCCACCCCCACTGA;RSEQ=GCAGGGACTTGTTCTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1793:1778:597,1181:1,1:2,1778:0.9916:2,2:38:1:33.7:1:1:1.97747:60:40.349:0.9948:0.0519:1.2 1/1:1821:1802:631,1171:2,0:2,1802:0.9896:0,2:37.2:1:33.8:1:0.123:0:60:59.067:0.9938:0.0417:1.2
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chr20 43964288 43964288 T C intronic SDC4 . . . rs2072792 . 437785 Type_2_diabetes_mellitus Human_Phenotype_Ontology:HP:0005965,Human_Phenotype_Ontology:HP:0005978,Human_Phenotype_Ontology:HP:0100652,MONDO:MONDO:0005148,MeSH:D003924,MedGen:C0011860,OMIM:125853,SNOMED_CT:44054006 no_assertion_criteria_provided Benign 0.495008 0.5149 . . . . . . . . . 0.4862 0.3876 0.6304 0.5133 0.5664 0.5307 0.5157 0.4887 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 393 2967 chr20 43964288 . T C 393 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2947;VD=2937;AF=0.9966;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=7.40642;LSEQ=TACTTTTGTTTCCCCTTTTT;RSEQ=TGAGAAGGAAGAAGGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2947:2937:1780,1157:1,0:1,2937:0.9966:0,2:39:1:34.2:1:1:0:60:58.939:0.9965:0.0251:1.3 1/1:2967:2894:1709,1185:1,0:1,2894:0.9754:0,2:38.8:1:34.4:1:1:0:60:95.467:0.9958:0.0226:1.3
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chr20 43964407 43964407 G C intron SDC4 NM_002999:exon2:c.199+15C>G . . rs2072791 ID=COSV65595683;OCCURENCE=1(skin) . . . . . 0.769369 0.9554 0.7280 0.7723 0.6528 0.8003 0.9638 0.7972 0.7649 0.7853 0.7409 0.7446 0.6624 0.7912 0.7067 0.9618 0.7983 0.7548 0.7377 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.12 1 389 2397 chr20 43964407 . G C 389 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2580;VD=2570;AF=0.9961;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52245;SOR=1.07662;LSEQ=TTTGTGCCTACGCCTGCCCA;RSEQ=CACACCTTCCGTACCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2580:2570:1240,1330:1,1:2,2570:0.9961:2,2:37.8:1:34.4:1:1:1.07252:60:90.786:0.998:0.0372:1.3 1/1:2397:2387:1115,1272:0,0:0,2387:0.9958:0,2:38.6:1:34.3:1:1:0:60:78.567:0.9979:0.0209:1.3
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chr20 57600655 57600655 G C UTR3 ATP5F1E;TUBB1 NM_006886:c.*3245C>G;NM_030773:c.*817G>C . . rs10485828 . . . . . . 0.125998 0.1468 . . . . . . . . . 0.1287 0.0329 0.1623 0.1623 0.1489 0.1435 0.1746 0.1534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20q13.32 0.5 348 2101 chr20 57600655 . G C 348 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2233;VD=1144;AF=0.5123;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06476;SOR=1.09856;LSEQ=TCCTTGGCTTTCCTTTTAAA;RSEQ=GCTATTTTGAAATGGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2233:1144:634,510:646,440:1086,1144:0.5123:2,2:40.2:1:34.3:1:0.05397:1.18094:60:66.294:0.5111:0.0076:1.1 0/1:2101:1027:622,405:625,445:1070,1027:0.4888:2,2:40.5:1:34.5:1:0.3278:1.09:60:170.167:0.4904:0.0048:1.1
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chr21 46957794 46957794 T C exonic SLC19A1 . nonsynonymous SNV SLC19A1:NM_001205206:exon2:c.80A>G:p.H27R,SLC19A1:NM_001352511:exon2:c.80A>G:p.H27R,SLC19A1:NM_001352512:exon2:c.80A>G:p.H27R,SLC19A1:NM_194255:exon2:c.80A>G:p.H27R rs1051266 ID=COSV60752997;OCCURENCE=1(central_nervous_system),2(urinary_tract),1(lung),2(thyroid) 167450 Gastrointestinal_stromal_tumor|methotrexate_response_-_Efficacy Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MedGen:CN236565 reviewed_by_expert_panel drug_response 0.488618 0.4742 0.5093 0.5783 0.4173 0.5905 0.5190 0.6026 0.5974 0.5961 0.6063 0.5113 0.3908 0.5622 0.61 0.4765 0.5385 0.5699 0.5761 0.346 0.129 T 0.403 0.045 N 1.000 0.090 P -1.445 0.006 N -1.39 0.850 T -0.61 0.181 N -0.984 0.340 T 0.000 0.000 T . . . . . 0.066 0.124 N c -1.071 -0.952 0.999 0.398 0.732 0.924 0 2.77 0.315 0.987 0.290 -0.075 0.119 0.016 0.191 0.106 0.191 4.720 0.122 Major facilitator superfamily domain ENSG00000173638.14 Skin_Sun_Exposed_Lower_leg 21q22.3 0.5 345 2129 chr21 46957794 . T C 345 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2200;VD=1081;AF=0.4914;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02991;SOR=0.89021;LSEQ=AGCAAAGGTAGCACACGAGG;RSEQ=GCCGCCAGGACCGGAGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2200:1081:717,364:728,377:1105,1081:0.4914:2,2:39.9:1:34.4:1:0.85658:1.02:60:66.562:0.4915:0.0145:1.3 1/0:2129:1108:722,386:672,343:1015,1108:0.5204:2,2:40.3:1:34.2:1:0.61513:1.04743:60:68.25:0.5212:0.0155:1.3
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chr22 29104955 29104955 A C intronic CHEK2 . . . rs5762756 ID=COSV60426587;OCCURENCE=1(haematopoietic_and_lymphoid_tissue) . . . . . 0.574481 0.6835 . 0.5978 0.37 0.5795 0.6786 0.6916 0.5637 0.5522 0.5908 0.5875 0.4176 0.6210 0.6866 0.7741 0.6654 0.6456 0.6498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q12.1 0.5 311 905 chr22 29104955 . A C 311 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=955;VD=656;AF=0.6869;SHIFT3=1;MSI=22.000;MSILEN=1;SSF=0.45152;SOR=0.98291;LSEQ=CGTCTCAAAAAAAAAAAAAA;RSEQ=AAAAAAACAAACAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:955:656:425,231:206,84:290,656:0.6869:2,2:40.9:1:33.3:1:0.06182:1.33254:60:33.526:0.6901:0:2.1 1/0:905:625:412,213:199,78:277,625:0.6906:2,2:39.5:1:33.5:1:0.08935:1.31859:60:27.409:0.686:0.0033:2.1
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chr22 29104959 29104959 A C intronic CHEK2 . . . rs5762757 . . . . . . 0.584265 0.6935 . 0.6012 0.3462 0.6023 0.7054 0.7046 0.5733 0.5141 0.5904 0.5978 0.4271 0.6349 0.7482 0.7761 0.6784 0.6553 0.6549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q12.1 0.5 312 948 chr22 29104959 . A C 312 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=981;VD=675;AF=0.6881;SHIFT3=1;MSI=22.000;MSILEN=1;SSF=0.48561;SOR=0.99164;LSEQ=TCAAAAAAAAAAAAAAAAAA;RSEQ=AAACAAACAAAAAAAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:981:675:437,238:216,88:304,675:0.6881:2,2:41.5:1:33.3:1:0.05679:1.33641:60:29.682:0.6831:0:2.1 1/0:948:654:427,227:211,82:293,654:0.6899:2,2:39.2:1:33.6:1:0.04314:1.36749:60:39.875:0.6882:0.0222:2.1
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chr22 29104968 29104968 A - intronic CHEK2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q12.1 0.5 145 1026 chr22 29104967 . CA C 145 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=1093;VD=12;AF=0.011;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.13687;SOR=0.62179;LSEQ=AAAAAAAAAAAAAAAACAAA;RSEQ=AAAAAAATGCCAGAATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1093:12:9,3:717,364:1081,12:0.011:2,2:40.3:1:35:1:0.76028:1.52:60:24:0.011:0.0009:1.2 0/1:1026:18:10,8:690,316:1006,18:0.0175:2,2:38.8:1:35:1:0.3053:1.74583:60:36:0.0176:0.001:1.6
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chr22 29120925 29120925 - A intron CHEK2 NM_007194:exon4:c.592+40->T;NM_001349956:exon4:c.445-14->T;NM_145862:exon4:c.592+40->T;NM_001257387:exon4:UTR5;NM_001005735:exon5:c.721+40->T . . rs745525787 ID=COSV60427898;OCCURENCE=1(prostate) . . . . . . . 0.0046 0.0039 0.0032 0.0055 0.0025 0.0003 0.0043 0.0052 0.0040 0.0001 0 0 0 0 0 0.0002 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q12.1 0.5 246 2187 chr22 29120925 . G GA 246 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=2177;VD=132;AF=0.0606;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.31255;SOR=1.07384;LSEQ=TTTCCTCCTATGAGAGAGTG;RSEQ=AAAAAAAAAATTCCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2177:132:77,55:959,721:1680,132:0.0606:2,2:44.2:1:35:0:0.85512:1.05:60:264:0.0807:0:0.1 0/1:2187:124:76,47:1046,774:1820,124:0.0567:2,2:43:1:34.7:1:0.39614:1.20:60:122:0.07:0:0.1
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chr22 42524908 42524908 C - exonic CYP2D6 . stopgain CYP2D6:NM_001025161:exon3:c.391delG:p.V131*,CYP2D6:NM_000106:exon4:c.544delG:p.V182* . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q13.2 0.25 186 2725 chr22 42524908 . C <DEL> 186 PASS STATUS=StrongLOH;SAMPLE=NCCL202312;TYPE=DEL;DP=2797;VD=0;AF=0;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=GGAGGCGATCACGTTGCTCA;RSEQ=GCTCACGGCTTTGTCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2797:0:0,0:1546,1250:2796,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 0/1:2725:42:21,21:1552,1168:2720,42:0.0154:2,2:75:1:34.5:1:0.43272:1.32861:57:84:0.0153:0.0154:2.3
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chr22 42524910 42524910 G - exonic CYP2D6 . stopgain CYP2D6:NM_001025161:exon3:c.389delC:p.V131*,CYP2D6:NM_000106:exon4:c.542delC:p.V182* . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q13.2 0.25 164 2742 chr22 42524910 . G <DEL> 164 PASS STATUS=StrongSomatic;SAMPLE=NCCL202312;TYPE=DEL;DP=2798;VD=34;AF=0.0122;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGGCGATCACGTTGCTCACG;RSEQ=CTCGAAGCGGCGCCCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2798:34:17,17:1566,1232:2798,34:0.0122:2,2:75:1:32.4:1:0.49271:1.27099:56:68:0.0122:0.0122:1.8 0/0:2742:0:0,0:1571,1170:2741,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0
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chr22 42524947 42524947 C T splicing CYP2D6 NM_001025161:exon3:c.353-1G>A;NM_000106:exon4:c.506-1G>A . . rs3892097 ID=COSV62243440;OCCURENCE=1(breast),6(soft_tissue) 31928 Debrisoquine,_poor_metabolism_of|Tamoxifen_response|Tramadol_response|not_specified|Deutetrabenazine_response|not_provided MedGen:C1837156|MedGen:CN078013|MedGen:CN078023|MedGen:CN169374|MedGen:CN258189|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Likely_benign|_drug_response|_other 0.0930511 0.002 0.1510 0.1678 0.1270 0.1563 0.0026 0.1548 0.2399 0.1402 0.1162 0.1363 0.0763 0.1123 0.2053 0.0037 0.1097 0.1912 0.1387 . . . . . . 1e-37 0.810 P . . . . . . . . . . . . . . . . . . . . 0.939 0.593 D c 0.757 0.496 0.998 0.365 0.162 0.029 0 3.37 0.375 5.880 0.692 0.810 0.333 1.000 0.715 0.093 0.186 10.491 0.437 . ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000100197.16|ENSG00000183172.8|ENSG00000100197.16|ENSG00000226450.2|ENSG00000100197.16|ENSG00000183066.10|ENSG00000183172.8|ENSG00000184983.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183172.8|ENSG00000100197.16|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000232710.1|ENSG00000205702.6|ENSG00000205704.5|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000232710.1|ENSG00000205702.6|ENSG00000226450.2|ENSG00000183066.10|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183172.8|ENSG00000100197.16|ENSG00000227370.1|ENSG00000205702.6|ENSG00000227370.1|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000100147.9|ENSG00000183066.10|ENSG00000215347.3|ENSG00000198951.7|ENSG00000183172.8|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000227370.1|ENSG00000183066.10|ENSG00000183172.8|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000227370.1|ENSG00000215347.3|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183066.10|ENSG00000183172.8|ENSG00000184983.5|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183066.10|ENSG00000198951.7|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000237037.5|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000227370.1|ENSG00000198911.7|ENSG00000183066.10|ENSG00000237037.5|ENSG00000233903.2|ENSG00000273366.1|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000227370.1|ENSG00000205702.6|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000226450.2 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Anterior_cingulate_cortex_BA24|Brain_Caudate_basal_ganglia|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hippocampus|Brain_Hippocampus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Lung|Lung|Lung|Lung|Lung|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Pancreas|Pituitary|Pituitary|Pituitary|Pituitary|Prostate|Prostate|Prostate|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Stomach|Stomach|Stomach|Testis|Testis|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Thyroid|Thyroid|Thyroid|Whole_Blood|Whole_Blood|Whole_Blood 22q13.2 0.5 356 2745 chr22 42524947 . C T 356 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2729;VD=1284;AF=0.4705;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23753;SOR=0.96065;LSEQ=GTTGGGGCGAAAGGGGCGTC;RSEQ=TGGGGGTGGGAGATGCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2729:1284:702,582:734,704:1438,1284:0.4705:2,2:41.1:1:34.5:1:0.05962:1.16:52:159.5:0.4722:0.0117:1.1 0/1:2745:1319:779,540:764,653:1417,1319:0.4805:2,2:39:1:34.4:1:0.00694:1.23:53:81.438:0.4805:0.0157:1.2
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chr22 42526694 42526694 G A exonic CYP2D6 . nonsynonymous SNV CYP2D6:NM_000106:exon1:c.100C>T:p.P34S,CYP2D6:NM_001025161:exon1:c.100C>T:p.P34S rs1065852 ID=COSV62243216;OCCURENCE=1(biliary_tract),1(haematopoietic_and_lymphoid_tissue),7(soft_tissue),1(kidney),1(pancreas) 31932 Debrisoquine,_poor_metabolism_of|Tamoxifen_response|Tramadol_response|not_specified|Deutetrabenazine_response|not_provided MedGen:C1837156|MedGen:CN078013|MedGen:CN078023|MedGen:CN169374|MedGen:CN258189|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Likely_benign|_drug_response|_other 0.238019 0.5714 0.1885 0.2461 0.1527 0.1507 0.5915 0.1563 0.2513 0.1808 0.1807 0.1921 0.1214 0.1343 0.2667 0.5812 0.1197 0.2110 0.1778 0.023 0.546 D 0.000 0.629 D 0.000 0.588 P 4.08 0.973 H -1.77 0.837 D -7.36 0.946 D -1.130 0.018 T 0.000 0.000 T . . . . . 0.985 0.833 D c 0.716 0.553 1.000 0.747 0.660 0.495 0 3.46 0.386 7.374 0.787 0.907 0.419 1.000 0.715 0.255 0.229 14.696 0.686 . ENSG00000183066.10|ENSG00000183172.8|ENSG00000184983.5|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000237037.5|ENSG00000100197.16|ENSG00000183172.8|ENSG00000100197.16|ENSG00000226450.2|ENSG00000100197.16|ENSG00000183066.10|ENSG00000183172.8|ENSG00000184983.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183172.8|ENSG00000100197.16|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000232710.1|ENSG00000205702.6|ENSG00000205704.5|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000232710.1|ENSG00000205702.6|ENSG00000226450.2|ENSG00000183066.10|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183172.8|ENSG00000100197.16|ENSG00000100197.16|ENSG00000183172.8|ENSG00000227370.1|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100147.9|ENSG00000183066.10|ENSG00000198951.7|ENSG00000183172.8|ENSG00000184983.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183066.10|ENSG00000184983.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000100197.16|ENSG00000227370.1|ENSG00000100197.16|ENSG00000183066.10|ENSG00000183172.8|ENSG00000184983.5|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183066.10|ENSG00000198951.7|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000183066.10|ENSG00000183172.8|ENSG00000184983.5|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183066.10|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000237037.5|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000198911.7|ENSG00000183066.10|ENSG00000237037.5|ENSG00000233903.2|ENSG00000273366.1|ENSG00000183066.10|ENSG00000183172.8|ENSG00000237037.5|ENSG00000100197.16|ENSG00000227370.1|ENSG00000226450.2|ENSG00000183172.8|ENSG00000100197.16|ENSG00000226450.2 Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Adrenal_Gland|Adrenal_Gland|Artery_Aorta|Artery_Aorta|Artery_Aorta|Artery_Coronary|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Artery_Tibial|Brain_Anterior_cingulate_cortex_BA24|Brain_Anterior_cingulate_cortex_BA24|Brain_Caudate_basal_ganglia|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Frontal_Cortex_BA9|Brain_Hippocampus|Brain_Hippocampus|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_EBV-transformed_lymphocytes|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Colon_Sigmoid|Colon_Sigmoid|Colon_Sigmoid|Colon_Transverse|Colon_Transverse|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Esophagus_Muscularis|Esophagus_Muscularis|Esophagus_Muscularis|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Lung|Lung|Lung|Lung|Lung|Lung|Lung|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Nerve_Tibial|Ovary|Ovary|Pancreas|Pancreas|Pituitary|Pituitary|Pituitary|Pituitary|Prostate|Prostate|Prostate|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Stomach|Stomach|Stomach|Stomach|Testis|Testis|Testis|Testis|Testis|Thyroid|Thyroid|Thyroid|Thyroid|Thyroid|Thyroid|Whole_Blood|Whole_Blood|Whole_Blood 22q13.2 0.5 390 3750 chr22 42526694 . G A 390 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=3820;VD=2509;AF=0.6568;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50942;SOR=1;LSEQ=CAGTGGCAGGGGGCCTGGTG;RSEQ=GTAGCGTGCAGCCCAGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3820:2509:1500,1009:752,551:1303,2509:0.6568:2,2:39.8:1:34.6:1:0.22428:1.09:60:108.087:0.6584:0.0008:1.3 1/0:3750:2463:1431,1032:773,511:1284,2463:0.6568:2,2:38.8:1:34.6:1:0.22105:1.0909:60:204.25:0.6612:0.008:1.3
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chr22 44324676 44324676 A G intron PNPLA3 NM_025225:exon3:c.421-28A>G . . rs139051 ID=COSV53379453;OCCURENCE=1(breast) . . . . . 0.516374 0.374 0.6186 0.5612 0.5963 0.3242 0.3704 0.6376 0.6276 0.6282 0.5413 0.5978 0.5980 0.3944 0.6747 0.3687 0.6347 0.6234 0.6064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22q13.31 1 384 2177 chr22 44324676 . A G 384 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=SNV;DP=2222;VD=2212;AF=0.9955;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16003;SOR=0.50929;LSEQ=TTAAAAGGGTGCTCTCGCCT;RSEQ=TAACTTCTCTCTCCTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2222:2212:1346,866:0,1:1,2212:0.9955:0,2:39.4:1:34.6:1:0.39178:0:60:169.154:0.9995:0.0581:1.1 1/1:2177:2172:1320,852:0,0:0,2172:0.9977:0,2:40.6:1:34.7:1:1:0:60:216.2:0.9995:0.0432:1.1
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chrX 66765155 66765158 TGCT AGCA exonic AR . nonframeshift substitution AR:NM_000044:exon1:c.167_170delinsAGCA:p.L56_L57delinsQQ,AR:NM_001348061:exon1:c.167_170delinsAGCA:p.L56_L57delinsQQ,AR:NM_001348063:exon1:c.167_170delinsAGCA:p.L56_L57delinsQQ,AR:NM_001348064:exon1:c.167_170delinsAGCA:p.L56_L57delinsQQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xq12 0.5 222 1723 chrX 66765155 . TGCT AGCA 222 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Complex;DP=1659;VD=71;AF=0.0431;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.16386;SOR=0.8408;LSEQ=TCCCGGCGCCAGTTTGCTGC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1659:71:51,20:977,575:1552,71:0.0431:2,2:11.1:1:35:1:0.1654:1.50:60:142:0.0435:0.0128:1.9 0/1:1723:87:66,21:1088,576:1664,87:0.0494:2,2:11.3:1:34.5:1:0.04841:1.66:60:174:0.0497:0.0182:1.8
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chrX 66765158 66765158 - GCAGCA exonic AR . nonframeshift insertion AR:NM_000044:exon1:c.170_171insGCAGCA:p.Q80_E81insQQ,AR:NM_001348061:exon1:c.170_171insGCAGCA:p.Q80_E81insQQ,AR:NM_001348063:exon1:c.170_171insGCAGCA:p.Q80_E81insQQ,AR:NM_001348064:exon1:c.170_171insGCAGCA:p.Q80_E81insQQ rs3032358 ID=COSV65953707;OCCURENCE=4(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(upper_aerodigestive_tract) 274659 not_specified|not_provided MedGen:CN169374|MedGen:CN517202 criteria_provided,_multiple_submitters,_no_conflicts Benign . . . . . . . . . . . 0.0892 0.0468 0.0959 0.1163 0.1154 0.0843 0.1127 0.0909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xq12 0.5 308 1751 chrX 66765158 . T TGCAGCA 308 PASS STATUS=Germline;SAMPLE=NCCL202312;TYPE=Insertion;DP=1696;VD=385;AF=0.227;SHIFT3=69;MSI=25.000;MSILEN=3;SSF=0.01505;SOR=0.83901;LSEQ=CGGCGCCAGTTTGCTGCTGC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1696:385:261,123:124,76:200,385:0.227:2,2:31.2:1:34.8:1:0.16763:1.30:60:770:1:0.0348:0.2 0/1:1751:454:311,143:134,74:208,454:0.2593:2,2:32.9:1:34.9:1:0.32671:1.20:60:908:1:0.0337:0.2
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chrX 66765243 66765245 GCA - exonic AR . nonframeshift deletion AR:NM_000044:exon1:c.255_257del:p.Q91del,AR:NM_001348061:exon1:c.255_257del:p.Q91del,AR:NM_001348063:exon1:c.255_257del:p.Q91del,AR:NM_001348064:exon1:c.255_257del:p.Q91del rs753526329 ID=COSV65954891;OCCURENCE=1(salivary_gland),1(breast),1(pleura),1(haematopoietic_and_lymphoid_tissue),1(stomach) . . . . . . . 0.0378 0.0038 0.0030 0.0065 0.0052 0.0009 0.0040 0.0102 0.0021 0 0 0 0 0 0 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xq12 0.5 222 2443 chrX 66765242 . GGCA G 222 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=Deletion;DP=2479;VD=82;AF=0.0331;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.28771;SOR=1.11061;LSEQ=GCAGCAAGAGACTAGCCCCA;RSEQ=GCAGCAGCAGCAGCAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2479:82:57,25:1536,851:2387,82:0.0331:2,2:34.4:1:35:1:0.41129:1.26:60:164:0.0334:0.004:0.3 0/1:2443:73:47,26:1538,821:2359,73:0.0299:2,2:36.2:1:34.7:1:0.90105:1.03626:60:146:0.0303:0.0053:0.2
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chrX 66766347 66766350 TGGG GGGT exonic AR . nonframeshift substitution AR:NM_000044:exon1:c.1359_1362delinsGGGT:p.G453G,AR:NM_001348061:exon1:c.1359_1362delinsGGGT:p.G453G,AR:NM_001348063:exon1:c.1359_1362delinsGGGT:p.G453G,AR:NM_001348064:exon1:c.1359_1362delinsGGGT:p.G453G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xq12 0.5 170 2765 chrX 66766347 . TGGG GGGT 170 PASS STATUS=LikelyLOH;SAMPLE=NCCL202312;TYPE=Complex;DP=2775;VD=31;AF=0.0112;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49423;SOR=0.96486;LSEQ=TATGGACCGTGTGGTGGTGG;RSEQ=GGTGGTGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2775:31:22,9:1473,1260:2733,31:0.0112:2,2:4.9:1:35:1:0.06951:2.09:60:62:0.0114:0.0108:0.7 0/1:2765:32:19,13:1422,1230:2652,32:0.0116:2,2:8.4:1:34.1:1:0.59441:1.26:60:64:0.0121:0.0105:1.3
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chrX 66766356 66766356 T C exonic AR . synonymous SNV AR:NM_000044:exon1:c.1368T>C:p.G456G,AR:NM_001348061:exon1:c.1368T>C:p.G456G,AR:NM_001348063:exon1:c.1368T>C:p.G456G,AR:NM_001348064:exon1:c.1368T>C:p.G456G rs866187574 ID=COSV65955683;OCCURENCE=1(liver),4(skin),1(lung) 694915 Kennedy_disease|Androgen_resistance_syndrome|not_provided MONDO:MONDO:0010735,MedGen:C1839259,OMIM:313200,Orphanet:ORPHA481|MONDO:MONDO:0019154,MedGen:C0039585,OMIM:300068,Orphanet:ORPHA754,SNOMED_CT:12313004|MedGen:CN517202 criteria_provided,_single_submitter Likely_benign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xq12 0.5 201 2631 chrX 66766356 . T C 201 PASS STATUS=LikelySomatic;SAMPLE=NCCL202312;TYPE=SNV;DP=2637;VD=59;AF=0.0224;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50498;SOR=1.01527;LSEQ=TGTGGTGGTGGTGGGGGTGG;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2637:59:42,17:1385,1187:2572,59:0.0224:2,2:7.3:1:34.2:1:0.00813:2.12:60:28.5:0.0223:0:1.1 0/1:2631:58:36,22:1371,1193:2564,58:0.022:2,2:10.5:1:32.8:1:0.23086:1.42:60:28:0.0219:0:1.3
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