ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.9592T>C (p.Cys3198Arg) (rs80359229)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000587762 SCV000885108 benign not provided 2017-07-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV000163019 SCV000213507 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000031835 SCV000147671 uncertain significance Breast-ovarian cancer, familial 2 2004-02-20 no assertion criteria provided clinical testing
Color RCV000163019 SCV000684076 likely benign Hereditary cancer-predisposing syndrome 2015-07-22 criteria provided, single submitter clinical testing
Counsyl RCV000031835 SCV000487886 benign Breast-ovarian cancer, familial 2 2015-12-04 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000031835 SCV000244495 benign Breast-ovarian cancer, familial 2 2015-08-10 reviewed by expert panel curation IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.00000368
GeneDx RCV000421898 SCV000517305 likely benign not specified 2017-10-24 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. RCV000045863 SCV000267850 likely benign Hereditary breast and ovarian cancer syndrome 2016-04-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587762 SCV000695255 likely benign not provided 2017-02-10 criteria provided, single submitter clinical testing Variant summary: Variant affects a non-conserved nucleotide and results in a replacement of a medium size and polar Cysteine (C) with large size and basic Arginine (R). 3/5 in silico tools predict the variant to be benign. It was observed exclusively in the European (Non-Finnish) subcohorts of the ExAC project at an allele frequency of 0.0074% which does not exceed the maximal expected allele frequency of a disease causing BRCA2 allele (0.075%). To our knowledge, the variant was not reported in HBOC spectrum patients via publications that demonstrate strong evidence for pathogenicity. In vitro/vivo studies assessing the effect of the variant on the function of the protein were not published either at the time of scoring. BIC lists a patient in whom the variant co-occurred with a potentially pathogenic BRCA2 variant c.748_748delG (p.Val250Terfs) indicating a neutral impact. Moreover, large genetic and probabilistic analyses show odds in favor of neutrality or very low odds in favor of causality and clinical diagnostic laboratories classify variant as Likely Benign/Benign via ClinVar (without evidence to independently evaluate). Considering all evidence, the variant was classified as Likely Benign.
Invitae RCV000045863 SCV000073876 likely benign Hereditary breast and ovarian cancer syndrome 2017-12-21 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587762 SCV000887971 benign not provided 2018-08-22 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031835 SCV000054443 benign Breast-ovarian cancer, familial 2 2012-05-01 no assertion criteria provided clinical testing

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