ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.5879G>A (p.Cys1960Tyr) (rs56157628)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000044781 SCV000602749 likely benign not specified 2016-09-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV000130706 SCV000185593 likely benign Hereditary cancer-predisposing syndrome 2017-08-11 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Other data supporting benign classification,In silico models in agreement (benign)
Breast Cancer Information Core (BIC) (BRCA2) RCV000031584 SCV000146721 uncertain significance Breast-ovarian cancer, familial 2 2004-02-20 no assertion criteria provided clinical testing
Color RCV000130706 SCV000683737 likely benign Hereditary cancer-predisposing syndrome 2015-10-26 criteria provided, single submitter clinical testing
GeneDx RCV000044781 SCV000210621 likely benign not specified 2017-08-28 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 RCV000590316 SCV000694910 benign not provided 2017-03-07 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.5879G>A (p.Cys1960Tyr) variant involves the alteration of a non-conserved nucleotide. The variant is located outside of any know functional domain or repeat and 3/5 in silico tools predict a benign outcome for this variant. This variant was found in 17/120980 control chromosomes of ExAC, predominantly observed in the African subpopulation at a frequency of 0.001587 (16/10082). 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 the populations of African origin. The variant is present in a control population dataset of gnomAD at a frequency of 0.0001372 (38/277020 chrs), mainly in individuals of African origin: 0.0015 (36/24015 chrs, including 7 homozygotes). This data support the speculation that the variant of interest may be an ethnic-specific functional polymorphism. The variant has been reported in affected individuals via publications with limited information (no co-occurrence or co-segregation information provided). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Furthermore, ClinVar - SCRP (RCV000031584.4) cites the variant to co-occur with pathogenic BRCA1 variants, 3555del4 and IVS23+1G>A. In addition, the variant was identified to co-occure with a known pathogenic variant in BRCA1 c.4357+1G>A/IVS12+1G>T, further supporting the non-pathogenic role of c.58769G>A variant. Taken together, this variant is classified as benign.
Invitae RCV000167827 SCV000072794 benign Hereditary breast and ovarian cancer syndrome 2018-01-08 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000044781 SCV000600666 likely benign not specified 2016-11-26 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000590316 SCV000889082 likely benign not provided 2018-04-06 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031584 SCV000054190 benign Breast-ovarian cancer, familial 2 2012-05-01 no assertion criteria provided clinical testing

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