ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.4656T>C (p.Gly1552=)

gnomAD frequency: 0.00009  dbSNP: rs41293491
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Total submissions: 17
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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) RCV000113328 SCV000578870 likely benign Breast-ovarian cancer, familial, susceptibility to, 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/).
Invitae RCV001085696 SCV000072476 benign Hereditary breast ovarian cancer syndrome 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV000589392 SCV000167368 likely benign not provided 2021-04-05 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 15307796, 25710373, 20858050, 8665505)
Ambry Genetics RCV000131764 SCV000186808 likely benign Hereditary cancer-predisposing syndrome 2014-08-11 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Counsyl RCV000113328 SCV000220860 likely benign Breast-ovarian cancer, familial, susceptibility to, 2 2014-11-07 criteria provided, single submitter literature only
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000123975 SCV000538479 likely benign not specified 2016-12-02 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant has not been reported in affected individuals. It is present in HGMD (classified as DM) in a publication describing a method for detecting variants. This variant is classified in ClinVar with 1 star as Benign or Likely Benign by 5 submitters: BIC, Invitae, Ambry, GeneDx, Counsyl. It is present in ExAC with a Max MAF of 0.009% (6 European alleles) and in gnomAD with a MaxMAF of 0.01% (14 European alleles).
Color Diagnostics, LLC DBA Color Health RCV000131764 SCV000683641 likely benign Hereditary cancer-predisposing syndrome 2015-07-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000123975 SCV000694792 likely benign not specified 2021-07-18 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000589392 SCV000805711 likely benign not provided 2017-02-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589392 SCV000889058 likely benign not provided 2023-01-09 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000123975 SCV001157015 likely benign not specified 2018-10-16 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario RCV001798234 SCV002043077 likely benign Breast and/or ovarian cancer 2022-08-15 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000131764 SCV002533888 likely benign Hereditary cancer-predisposing syndrome 2021-11-15 criteria provided, single submitter curation
Fulgent Genetics, Fulgent Genetics RCV002496689 SCV002805379 likely benign Familial cancer of breast; Breast-ovarian cancer, familial, susceptibility to, 2; Fanconi anemia complementation group D1; Medulloblastoma; Wilms tumor 1; Malignant tumor of prostate; Pancreatic cancer, susceptibility to, 2; Glioma susceptibility 3 2021-12-08 criteria provided, single submitter clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000123975 SCV004243033 likely benign not specified 2024-02-06 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000113328 SCV000146463 benign Breast-ovarian cancer, familial, susceptibility to, 2 2002-05-29 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353398 SCV000591917 benign Malignant tumor of breast no assertion criteria provided clinical testing The p.Gly1552Gly variant has been presented 7 times in the UMD and two times in the BIC database as having no clinical significance. It is listed in dbSNP database (ID#: rs41293491) coming from a “clinical source’ with an average heterozygosity of 0.000+/-0.015, therefore representing a rare variant in the population. This variant is not expected to have clinical significance because it does not alter an amino acid residue, and is not located near a splice junction. In summary, the clinical significance of this variant cannot be determined with certainty at this time, although we would lean towards a more benign role for this variant. This variant is classified as Benign.

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