ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.9270C>T (p.Phe3090=) (rs587780873)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163089 SCV000213592 likely benign Hereditary cancer-predisposing syndrome 2015-04-21 criteria provided, single submitter clinical testing
Baylor Genetics RCV000474408 SCV000541062 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Color RCV000163089 SCV000684045 likely benign Hereditary cancer-predisposing syndrome 2015-08-07 criteria provided, single submitter clinical testing
Counsyl RCV000410788 SCV000489390 likely benign Breast-ovarian cancer, familial 2 2016-09-29 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000724624 SCV000228186 uncertain significance not provided 2015-03-03 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000410788 SCV000579141 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 RCV000124014 SCV000167420 benign not specified 2014-03-19 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 RCV000124014 SCV000695229 likely benign not specified 2017-11-06 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.9270C>T (p.Phe3090Phe) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation Taster predicts a damaging outcome for this variant implicating “splice site changes”, however 5/5 splice prediction tools in Alamut predict no significant impact on normal splicing. ESE finder predicts that this variant may affect the binding site of the splicing factor SRp55, however a functional study found that the variant doesn’t affect splicing in lymphocytes (Quiles 2016). This variant was found in 8/276150 control chromosomes at a frequency of 0.000029, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). The variant, to our knowledge, has not been published in the literature as a germline variant in HBOC affected individuals, however the variant has been reported as a somatic mutation in a serous endometrial carcinoma and malignant melanomas (COSMIC). In addition, multiple clinical diagnostic laboratories classified this variant as benign or likely benign. Taken together, this variant is classified as likely benign.
Invitae RCV000229741 SCV000283362 benign Hereditary breast and ovarian cancer syndrome 2017-12-10 criteria provided, single submitter clinical testing

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