ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.3839A>T (p.Asp1280Val) (rs56337919)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000077315 SCV000244442 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 = 0.0000286
Invitae RCV000167824 SCV000072291 likely benign Hereditary breast and ovarian cancer syndrome 2018-01-03 criteria provided, single submitter clinical testing
GeneDx RCV000044278 SCV000210597 likely benign not specified 2018-01-12 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.
Ambry Genetics RCV000162783 SCV000213261 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing
Counsyl RCV000077315 SCV000487915 benign Breast-ovarian cancer, familial 2 2015-12-01 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587147 SCV000694722 likely benign not provided 2017-04-04 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.3839A>T (p.Asp1280Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. 2/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). The variant of interest has been found in a large, broad control population, ExAC in 1/96130 control chromosomes at a frequency of 0.0000104, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). Lindor_2012 calculated prior and posterior probabilities of the variant being deleterious, derived from an evolutionary sequence conservation model and likelihoods of causality derived from segregation, co-occurrence and the personal and family history of cancer, to be 0.02 and 2.86E-05, respectively. In addition, this variant is co-occurring with pathogenic variants in an internal specimen: BRCA1 c.66dupA/p.Glu23fsX18 and the a publication indicates the variant to have been found in an unaffected individual. This strongly suggests a benign outcome for this variant. Multiple peer-reviewed publications, reputable databases, and clinical laboratories have classified this variant as benign/likely benign; however without evidence for independent review. Taken together, this variant has been classified as "likely benign."
PreventionGenetics,PreventionGenetics RCV000587147 SCV000805700 likely benign not provided 2017-06-15 criteria provided, single submitter clinical testing
Color RCV000162783 SCV000902727 benign Hereditary cancer-predisposing syndrome 2016-05-02 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000077315 SCV000109112 benign Breast-ovarian cancer, familial 2 2009-10-22 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000077315 SCV000146306 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing

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