ClinVar Miner

Submissions for variant NM_007294.3(BRCA1):c.3717T>A (p.Ser1239=) (rs730881453)

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Total submissions: 6
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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) RCV000495015 SCV000578212 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 RCV000159881 SCV000209957 benign not specified 2014-07-07 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 RCV000165861 SCV000216610 likely benign Hereditary cancer-predisposing syndrome 2014-09-05 criteria provided, single submitter clinical testing
Invitae RCV000476167 SCV000560223 benign Hereditary breast and ovarian cancer syndrome 2017-10-27 criteria provided, single submitter clinical testing
Color RCV000165861 SCV000683126 benign Hereditary cancer-predisposing syndrome 2015-08-04 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586659 SCV000699064 likely benign not provided 2016-10-06 criteria provided, single submitter clinical testing Variant summary: The BRCA1 c.3717T>A (p.Ser1239Ser) 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, which was confirmed by a functional study (Anczukow_2008). This variant was found in 7/121392 control chromosomes at a frequency of 0.0000577, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA1 variant (0.0010005). This variant has been reported in multiple patients, including one patient who carries a potential pathogenic variant BRCA2 c.IVS6+2T>C (c.516+2T>C). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as likely benign.

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