ClinVar Miner

Submissions for variant NM_007294.3(BRCA1):c.5412C>T (p.Val1804=) (rs730881456)

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Total submissions: 9
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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) RCV000411366 SCV000578334 likely benign Breast-ovarian cancer, familial 1 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 RCV000159893 SCV000209993 benign not specified 2014-09-26 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 RCV000162643 SCV000213080 likely benign Hereditary cancer-predisposing syndrome 2014-10-13 criteria provided, single submitter clinical testing
Counsyl RCV000411366 SCV000488566 likely benign Breast-ovarian cancer, familial 1 2016-05-09 criteria provided, single submitter clinical testing
Invitae RCV000476616 SCV000560260 likely benign Hereditary breast and ovarian cancer syndrome 2017-12-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000159893 SCV000600421 likely benign not specified 2017-06-09 criteria provided, single submitter clinical testing
Color RCV000162643 SCV000683312 likely benign Hereditary cancer-predisposing syndrome 2016-11-16 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589790 SCV000699252 likely benign not provided 2017-04-06 criteria provided, single submitter clinical testing Variant summary: The BRCA1 5412C>T (p.Val1804Val) 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, while ESE finder predicts that this variant may create an SC35 ESE site at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in the large control database ExAC at a frequency of 0.0000082 (1/121552 control chromosomes), which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA1 variant (0.0010005). The variant has been cited in several studies of patient cohorts, typically classified by the authors as a benign or a variant of unknown clinical significance. In one study, the variant was identified within two independent families and did not cosegregate with disease, suggesting a benign impact for this variant (McKean-Cowdin_HumGen_2005). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign (2x) or benign (1x). Taken together, this variant is classified as likely benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589790 SCV000888946 likely benign not provided 2017-06-09 criteria provided, single submitter clinical testing

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