ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.2919G>A (p.Ser973=) (rs45525041)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162604 SCV000213028 likely benign Hereditary cancer-predisposing syndrome 2014-08-28 criteria provided, single submitter clinical testing
Baylor Genetics RCV000474196 SCV000541042 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000113113 SCV000146139 uncertain significance Breast-ovarian cancer, familial 2 2003-01-24 no assertion criteria provided clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000768592 SCV000219320 likely benign Breast and/or ovarian cancer 2015-12-11 criteria provided, single submitter clinical testing
Cancer Genetics and Genomics Laboratory,British Columbia Cancer Agency RCV000168560 SCV000586937 likely benign not specified 2017-04-18 criteria provided, single submitter clinical testing
Color RCV000162604 SCV000683511 likely benign Hereditary cancer-predisposing syndrome 2015-06-01 criteria provided, single submitter clinical testing
Counsyl RCV000113113 SCV000220910 likely benign Breast-ovarian cancer, familial 2 2014-11-24 criteria provided, single submitter literature only
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000113113 SCV000578022 benign Breast-ovarian cancer, familial 2 2017-06-29 reviewed by expert panel curation Synonymous substitution variant, with low bioinformatic likelihood to alter mRNA splicing (splicing prior 0.02; http://priors.hci.utah.edu/PRIORS/) and frequency 0.0018 (South Asian), derived from ExAC (2014-12-17).
GeneDx RCV000168560 SCV000167349 benign not specified 2014-02-06 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.
Illumina Clinical Services Laboratory,Illumina RCV000044085 SCV000383663 likely benign Hereditary breast and ovarian cancer syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000308141 SCV000383664 likely benign Fanconi anemia 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586047 SCV000694647 benign not provided 2016-10-18 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.2919G>A (p.Ser973Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 54/120514 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.0017597 (29/16480). This frequency is about 2.35 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. This variant is known to co-occur with multupe deleterious variants in literature (Lara_Biol Res_2012) and in UMD (BRCA1 c.5123C>A (p.Ala1708Glu), c.5266dup (p.Gln1756ProfsX74), c.2722G>T (p.Glu908X), and c.3485delA (p.Asp1162ValfsX48) and BRCA2 c.1184G>A (p.Trp395X)), strongly supporting for a benign outcome. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely beign. Taken together, this variant is classified as Benign.
Invitae RCV000044085 SCV000072098 benign Hereditary breast and ovarian cancer syndrome 2018-01-12 criteria provided, single submitter clinical testing

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