ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.7017G>C (p.Lys2339Asn) (rs45574331)

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Total submissions: 27
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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) RCV000113692 SCV000245106 benign Breast-ovarian cancer, familial 2 2015-01-12 reviewed by expert panel curation Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.02642 (African), derived from 1000 genomes (2012-04-30).
Invitae RCV000167851 SCV000073134 benign Hereditary breast and ovarian cancer syndrome 2020-12-08 criteria provided, single submitter clinical testing
Counsyl RCV000113692 SCV000154081 benign Breast-ovarian cancer, familial 2 2014-03-18 criteria provided, single submitter literature only
Ambry Genetics RCV000128918 SCV000172785 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing This alteration is classified as 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000120355 SCV000202294 benign not specified 2013-12-06 criteria provided, single submitter clinical testing
Pathway Genomics RCV000113692 SCV000223770 benign Breast-ovarian cancer, familial 2 2014-10-30 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000167851 SCV000257617 likely benign Hereditary breast and ovarian cancer syndrome 2015-04-14 criteria provided, single submitter clinical testing
Michigan Medical Genetics Laboratories,University of Michigan RCV000113692 SCV000267805 benign Breast-ovarian cancer, familial 2 2016-04-21 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000768605 SCV000324839 benign Breast and/or ovarian cancer 2016-01-26 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000383466 SCV000383754 likely benign Fanconi anemia, complementation group D1 2018-01-19 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000113692 SCV000383755 likely benign Breast-ovarian cancer, familial 2 2018-01-19 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000167851 SCV000494340 benign Hereditary breast and ovarian cancer syndrome 2014-04-15 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000120355 SCV000538462 benign not specified 2016-03-28 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: ExAC: 2.7% (262/9870) African chromosomes
Baylor Genetics RCV000465613 SCV000541038 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Cancer Genetics and Genomics Laboratory,British Columbia Cancer Agency RCV000120355 SCV000586971 benign not specified 2017-04-18 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282541 SCV000602876 benign none provided 2020-06-24 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000514662 SCV000610790 benign not provided 2017-05-30 criteria provided, single submitter clinical testing
Color Health, Inc RCV000128918 SCV000683843 benign Hereditary cancer-predisposing syndrome 2015-03-05 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000113692 SCV000744507 benign Breast-ovarian cancer, familial 2 2015-09-21 criteria provided, single submitter clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000128918 SCV000747801 likely benign Hereditary cancer-predisposing syndrome 2018-01-16 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000120355 SCV000805755 benign not specified 2017-04-13 criteria provided, single submitter clinical testing
ITMI RCV000120355 SCV000084507 not provided not specified 2013-09-19 no assertion provided reference population
Breast Cancer Information Core (BIC) (BRCA2) RCV000113692 SCV000147001 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353904 SCV000592091 benign Malignant tumor of breast no assertion criteria provided clinical testing The p.Lys2339Asn variant has been previously reported in the literature in 10/8236 proband chromosomes, and in none of the 132 control chromosomes tested (Capanu_2011_21520273, Gao_2000_11030417, Kote-Jarai_2011_21952622, Nanda_2005_16234499). It is listed in the dbSNP database as coming from a "clinical source" (ID#: rs45574331) with a MAF score of 0.006 (1000 Genomes). The variant was identified at high frequency >2.6% in African population from ExAC increasing likelihood this is a common benign polymorphism. The variant was also identified in the UMD (x19), BIC, Exome Server and the BOCs databases. In addition, in the UMD database, the p.Lys2339Asn variant was found to co-occur with a pathogenic mutation in BRCA1, c.2709_2710delTG (p.Cys903X), increasing the likelihood that the variant is a benign alteration. This residue is not conserved in mammals and computational analyses (SIFT, AlignGVGD) do not suggest a high likelihood of impact to the protein. However, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information, we cannot determine the clinical significance of this variant with certainty at this time, although we would lean towards a more benign role for this variant. In summary, this variant is classified as Benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000514662 SCV000778701 benign not provided 2017-12-23 no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000120355 SCV001906102 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000120355 SCV001956315 benign not specified no assertion criteria provided clinical testing

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