ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.3054G>A (p.Lys1018=) (rs368404583)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164199 SCV000214820 likely benign Hereditary cancer-predisposing syndrome 2015-02-26 criteria provided, single submitter clinical testing
Baylor Genetics RCV000462651 SCV000541072 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000495515 SCV000578823 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 RCV000123960 SCV000167352 benign not specified 2014-02-26 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.
Integrated Genetics/Laboratory Corporation of America RCV000123960 SCV000918961 uncertain significance not specified 2017-12-15 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.3054G>A (p.Lys1018Lys) variant involves the alteration of a non-conserved nucleotide located in a BRCA2 repeat (IPR002093), resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SC35. However, these predictions have yet to be confirmed by functional studies. This variant was found in 7/276540 control chromosomes, to date exclusively observed in the African subpopulation at a frequency of 0.000292 (7/23992), however this frequency does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). The variant of interest has not, to our knowledge, been reported in affected individuals via publications and is classified as benign/likely benign by multiple clinical laboratories. Taken together, this variant is classified as VUS-possibly benign.
Invitae RCV000226525 SCV000283203 likely benign Hereditary breast and ovarian cancer syndrome 2017-11-24 criteria provided, single submitter clinical testing
PreventionGenetics RCV000679166 SCV000805683 likely benign not provided 2017-10-20 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000679166 SCV000889014 likely benign not provided 2016-04-23 criteria provided, single submitter clinical testing

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