ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.9720T>C (p.Val3240=) (rs80359810)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162799 SCV000213280 likely benign Hereditary cancer-predisposing syndrome 2014-07-02 criteria provided, single submitter clinical testing
Baylor Genetics RCV000471010 SCV000541053 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000114157 SCV000147703 uncertain significance Breast-ovarian cancer, familial 2 2003-10-29 no assertion criteria provided clinical testing
Color RCV000162799 SCV000684088 likely benign Hereditary cancer-predisposing syndrome 2015-11-16 criteria provided, single submitter clinical testing
Counsyl RCV000114157 SCV000488763 likely benign Breast-ovarian cancer, familial 2 2016-06-09 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000045891 SCV000592304 likely benign not specified 2014-04-16 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000590764 SCV000228420 uncertain significance not provided 2015-05-22 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000114157 SCV000578960 likely benign Breast-ovarian cancer, familial 2 2017-06-29 reviewed by expert panel curation Synonymous substitution variant, with low bioinformatic likelihood to result in a splicing aberration (Splicing prior probability 0.02; http://priors.hci.utah.edu/PRIORS/).
GeneDx RCV000045891 SCV000210691 benign not specified 2014-07-21 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 RCV000167834 SCV000494411 likely benign Hereditary breast and ovarian cancer syndrome 2016-01-22 criteria provided, single submitter clinical testing Variant summary: The variant of interest causes a synonymous change involving a non-conserved nucleotide with 5/5 in silico programs via Alamut predicting no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC with an allele frequency of 10/121302 (1/12195), predominantly found in the African cohort, 10/10370 (1/1037), which exceeds the maximum expected allele frequency for a pathogenic BRCA2 variant of 1/1333. Therefore, suggesting that the variant of interest is a rare polymorphism specific to population(s) of African origin. The variant of interest has been reported in at least one affected individual via a publication, although with limited information (ie lack co-segregation data). However, an internal LCA sample reports the variant to co-occur with another probable pathogenic BRCA2 variant, c.2480dupA (p.N827fsX3 scored PrDV). In addition, multiple reputable clinical laboratories cite the variant with a classification of "likely benign/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as likely benign."
Integrated Genetics/Laboratory Corporation of America RCV000590764 SCV000695265 likely benign not provided 2016-01-22 criteria provided, single submitter clinical testing Variant summary: The variant of interest causes a synonymous change involving a non-conserved nucleotide with 5/5 in silico programs via Alamut predicting no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC with an allele frequency of 10/121302 (1/12195), predominantly found in the African cohort, 10/10370 (1/1037), which exceeds the maximum expected allele frequency for a pathogenic BRCA2 variant of 1/1333. Therefore, suggesting that the variant of interest is a rare polymorphism specific to population(s) of African origin. The variant of interest has been reported in at least one affected individual via a publication, although with limited information (ie lack co-segregation data). However, an internal LCA sample reports the variant to co-occur with another probable pathogenic BRCA2 variant, c.2480dupA (p.N827fsX3 classified as likely pathogenic). In addition, multiple reputable clinical laboratories cite the variant with a classification of "likely benign/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as likely benign.
Invitae RCV000167834 SCV000073904 benign Hereditary breast and ovarian cancer syndrome 2017-12-29 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000045891 SCV000600876 likely benign not specified 2017-02-14 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000590764 SCV000889189 benign not provided 2017-08-30 criteria provided, single submitter clinical testing

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