ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.6842-20T>A (rs81002811)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Breast Cancer Information Core (BIC) (BRCA2) RCV000031651 SCV000146960 uncertain significance Breast-ovarian cancer, familial 2 2004-02-20 no assertion criteria provided clinical testing
Color RCV000580943 SCV000683821 benign Hereditary cancer-predisposing syndrome 2015-12-29 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000031651 SCV000244468 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 = 0.000273
GeneDx RCV000212253 SCV000210638 benign not specified 2014-08-20 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.
Integrated Genetics/Laboratory Corporation of America RCV000590122 SCV000695001 benign not provided 2017-07-18 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.6842-20T>A variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a benign outcome for this variant. 4/5 in silico prediction tools predict no significant effect on splicing. This predicted result is supported by one published RT-PCR functional study (Menendez_2012) that this variant does not affect normal splicing. This variant was found in 56/234842 control chromosomes, predominantly observed in the Latino subpopulation at a frequency of 0.001314 (42/31970, 2 homozygotes). This frequency is about 2 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this is likely a benign polymorphism found primarily in population(s) of Latino origin. In clinical databases (BIC and UMD), the variant of interest was reported to co-occur with other BRCA1 deleterious variants (BRCA1 c.3756_3759delGTCT, c.5030_5033delCTAA (p.Thr1677IlefsX2) and p.Arg1203X) and a BRCA2 deleterious variant, c.7795_7797delGAA (p.Glu2599del), strongly suggesting for a benign outcome. Multifactorial probability based models also predict this variant to be benign. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely benign. Therefore, taking all lines of available evidence into consideration, the variant of interest is classified as "Benign.
Invitae RCV000045077 SCV000073090 benign Hereditary breast and ovarian cancer syndrome 2017-12-28 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031651 SCV000054258 benign Breast-ovarian cancer, familial 2 2008-11-01 no assertion criteria provided clinical testing

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