ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.6264T>C (p.Thr2088=) (rs750651726)

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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) RCV000495105 SCV000578942 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;
Invitae RCV000759638 SCV000259809 likely benign not provided 2019-02-22 criteria provided, single submitter clinical testing
GeneDx RCV000442483 SCV000519099 likely benign not specified 2015-10-23 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 RCV000445816 SCV000537485 likely benign Hereditary cancer-predisposing syndrome 2015-07-22 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000442483 SCV000592038 likely benign not specified 2014-03-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000445816 SCV000661205 likely benign Hereditary cancer-predisposing syndrome 2015-10-15 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759638 SCV000889094 likely benign not provided 2017-11-18 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000442483 SCV000916912 likely benign not specified 2017-09-11 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.6264T>C (p.Thr2088Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 10/120378 control chromosomes (1 homozygote) at a frequency of 0.0000831, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). This variant has been reported in HBOC patient and healthy elderly women. A small case-control study showed that the allele frequency of this variant is higher in controls than cases, suggesting this variant is benign. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. Taken together, this variant is classified as likely benign.

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