ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.627C>T (p.Leu209=) (rs28897704)

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Total submissions: 8
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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) RCV000495212 SCV000579140 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 RCV000160198 SCV000210548 benign not specified 2014-07-29 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 RCV000163068 SCV000213564 likely benign Hereditary cancer-predisposing syndrome 2014-09-08 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV001081531 SCV000253023 benign Hereditary breast and ovarian cancer syndrome 2020-11-05 criteria provided, single submitter clinical testing
Color Health, Inc RCV000163068 SCV000683765 likely benign Hereditary cancer-predisposing syndrome 2015-07-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000160198 SCV000694955 likely benign not specified 2020-09-06 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000589025 SCV000805736 likely benign not provided 2017-10-27 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000495212 SCV001553954 benign Breast-ovarian cancer, familial 2 no assertion criteria provided clinical testing The BRCA2 p.Leu209Leu variant was identified by Giacomo (Giacomo 2013) in an individual with Breast Cancer. The variant was also identified in dbSNP (ID: rs28897704) “With benign allele”, but no frequency information was provided, thus the prevalence of this variant in the general population could not be determined; in the Exome Aggregation Consortium (ExAC) database (released Oct 20th, 2014) in 2 of 121164 chromosomes (frequency: 0.0000) or 1 European (Non-Finnish) and 1 East Asian individuals, and none from a population of East Asian, Other, African, Latino, South Asian, and European (Finnish) individuals; the ClinVar database (classified as a benign variant by GeneDx and likely benign by Ambry Genetics), and UMD (1X as a 3-UV variant). The p.Leu209Leu variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. The BRCA2 p.Leu209Leu variant did not show exon skipping in functional assays combining minigene assays and analysis of patient RNA, contradicting the bioinformatics approach of using ESRseq scores to evaluate RNA hexamers as potential exonic splicing elements (Di Giacomo 2013). In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.

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