ClinVar Miner

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

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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) 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
Invitae RCV001084314 SCV000073090 benign Hereditary breast and ovarian cancer syndrome 2020-12-02 criteria provided, single submitter clinical testing
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.
Color Health, Inc RCV000580943 SCV000683821 benign Hereditary cancer-predisposing syndrome 2015-12-29 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 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.
Sharing Clinical Reports Project (SCRP) RCV000031651 SCV000054258 benign Breast-ovarian cancer, familial 2 2008-11-01 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000031651 SCV000146960 uncertain significance Breast-ovarian cancer, familial 2 2004-02-20 no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000212253 SCV001905938 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000212253 SCV001929642 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000212253 SCV001956434 benign not specified no assertion criteria provided clinical testing

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