ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.7806-40A>G

gnomAD frequency: 0.00858  dbSNP: rs9590939
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen RCV000113826 SCV004101439 benign Breast-ovarian cancer, familial, susceptibility to, 2 2023-10-12 reviewed by expert panel curation The c.7806-40A>G variant is an intronic variant occurring in intron 16 of the BRCA2 gene. The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth >=20) or gnomAD v3.1 (non-cancer subset, read depth >=20) is 0.02867 in the African/African American population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.001) for BA1 (BA1 met). This BRCA2 intronic variant is outside of the native donor and acceptor 1,2 splice sites, and SpliceAI predictor score of 0.00 suggests that the variant has no impact on splicing (score threshold <0.10) (BP4 met). This is an intronic variant, and mRNA experimental analysis indicates no impact on splicing (PMID: 22505045), considered strong evidence against pathogenicity (BP7_Strong (RNA)). This variant has been observed in >10 individuals with features considered inconsistent with an FA-associated phenotype, and (Likely) Pathogenic variant seen in trans or variant is homozygous (total score >4 points) (BS2 met; Invitae internal contributor). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.008 (based on Pathology LR=0.81; Case-Control LR=0.0095), within the thresholds for Strong benign evidence (LR >=0.00285 & <0.05) (BP5_Strong met; Internal lab contributors). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BA1, BP4, BP7_Strong (RNA), BS2, BP5_Strong).
Invitae RCV000045322 SCV000073335 benign Hereditary breast ovarian cancer syndrome 2023-08-17 criteria provided, single submitter clinical testing
Michigan Medical Genetics Laboratories, University of Michigan RCV000113826 SCV000196009 benign Breast-ovarian cancer, familial, susceptibility to, 2 2014-11-03 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000503364 SCV000592146 likely benign not specified 2017-10-25 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001594826 SCV000602769 benign not provided 2020-03-20 criteria provided, single submitter clinical testing
GeneDx RCV001594826 SCV001828157 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State RCV000045322 SCV002025832 benign Hereditary breast ovarian cancer syndrome 2022-04-19 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000113826 SCV004016865 benign Breast-ovarian cancer, familial, susceptibility to, 2 2023-07-07 criteria provided, single submitter clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000503364 SCV004243065 benign not specified 2024-02-06 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000113826 SCV000147194 uncertain significance Breast-ovarian cancer, familial, susceptibility to, 2 2007-01-18 no assertion criteria provided clinical testing
University of Washington Department of Laboratory Medicine, University of Washington RCV000209000 SCV000265020 likely benign Hereditary cancer-predisposing syndrome 2015-12-01 no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute RCV000503364 SCV001906393 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000503364 SCV001951979 benign not specified no assertion criteria provided clinical testing

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