ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.5828del (p.Ser1943fs) (rs80359541)

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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 RCV000622261 SCV000186291 pathogenic Inborn genetic diseases 2014-06-06 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: UNCERTAIN: Alteration(s) of Uncertain Clinical Significance Detected
Breast Cancer Information Core (BIC) (BRCA2) RCV000031580 SCV000146707 pathogenic Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Color RCV000131318 SCV000905018 pathogenic Hereditary cancer-predisposing syndrome 2017-11-20 criteria provided, single submitter clinical testing
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge RCV000031580 SCV000327291 pathogenic Breast-ovarian cancer, familial 2 2015-10-02 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000031580 SCV000300937 pathogenic Breast-ovarian cancer, familial 2 2016-09-08 reviewed by expert panel curation Variant allele predicted to encode a truncated non-functional protein.
GeneDx RCV000044766 SCV000210771 pathogenic not provided 2016-10-24 criteria provided, single submitter clinical testing This deletion of one nucleotide in BRCA2 is denoted c.5828delC at the cDNA level and p.Ser1943LeufsX20 (S1943LfsX20) at the protein level. The normal sequence, with the base that is deleted in brackets, is GTTT[delC]TAAA. The deletion causes a frameshift, which changes a Serine to a Leucine at codon 1943, and creates a premature stop codon at position 20 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. BRCA2 c.5828delC, also reported as 6056delC using alternate nomenclature, has been observed in association with breast and/or ovarian cancer (Palma 2008, Finkelman 2012). We consider this variant to be pathogenic.
Genetic Services Laboratory, University of Chicago RCV000031580 SCV000246807 pathogenic Breast-ovarian cancer, familial 2 2015-01-23 criteria provided, single submitter clinical testing
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. RCV000131318 SCV000679719 pathogenic Hereditary cancer-predisposing syndrome 2017-07-12 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000195355 SCV000694905 pathogenic Hereditary breast and ovarian cancer syndrome 2016-05-03 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.5828delC variant results in frameshift and a premature termination codon, predicted to cause a truncated or absent BRCA2 protein due to nonsense mediated decay, which is a commonly known mechanism for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. p.Ser1970X, p.Ser1982fs). Mutation Taster predicts damaging outcome for this variant. This variant was not found in 122374 control chromosomes, but has been cited in multiple cancer patients in the literature, including breast/ovarian and prostate cancers. In addition, clinical laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant was classified as pathogenic.
Invitae RCV000195355 SCV000072779 pathogenic Hereditary breast and ovarian cancer syndrome 2018-12-10 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser1943Leufs*20) in the BRCA2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 18703817, 22430266), and prostate cancer (PMID: 26681312). This variant is also known as 6056delC in the literature. ClinVar contains an entry for this variant (Variation ID: 37999). Loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). For these reasons, this variant has been classified as Pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000044766 SCV000296592 pathogenic not provided 2015-11-11 criteria provided, single submitter clinical testing
Research Molecular Genetics Laboratory,Women's College Hospital, University of Toronto RCV000195355 SCV000587803 pathogenic Hereditary breast and ovarian cancer syndrome 2014-01-31 no assertion criteria provided research
Sharing Clinical Reports Project (SCRP) RCV000031580 SCV000054186 pathogenic Breast-ovarian cancer, familial 2 2012-07-17 no assertion criteria provided clinical testing

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