ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.5070A>C (p.Lys1690Asn) (rs56087561)

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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000074533 SCV000602858 benign not specified 2017-02-08 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162621 SCV000213056 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000113374 SCV000146529 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000768596 SCV000219345 likely benign Breast and/or ovarian cancer 2017-01-18 criteria provided, single submitter clinical testing
Cancer Genetics and Genomics Laboratory,British Columbia Cancer Agency RCV000074533 SCV000586957 benign not specified 2017-04-18 criteria provided, single submitter clinical testing
Color RCV000162621 SCV000683669 likely benign Hereditary cancer-predisposing syndrome 2015-04-23 criteria provided, single submitter clinical testing
Counsyl RCV000113374 SCV000154079 likely benign Breast-ovarian cancer, familial 2 2014-03-07 criteria provided, single submitter literature only
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000113374 SCV000744461 benign Breast-ovarian cancer, familial 2 2017-05-31 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000074533 SCV000591937 benign not specified 2013-01-31 criteria provided, single submitter clinical testing
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000044548 SCV000257611 uncertain significance Hereditary breast and ovarian cancer syndrome 2015-04-17 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000113374 SCV000244454 benign Breast-ovarian cancer, familial 2 2015-08-10 reviewed by expert panel curation IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.0000000459
GeneDx RCV000074533 SCV000108618 likely benign not specified 2017-11-27 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.
Genetic Services Laboratory, University of Chicago RCV000074533 SCV000593746 uncertain significance not specified 2016-12-08 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000113374 SCV000743303 benign Breast-ovarian cancer, familial 2 2017-07-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587449 SCV000694825 benign not provided 2016-04-07 criteria provided, single submitter clinical testing Variant Summary: The c.5070A>C variant involves a conserved nucleotide in which 4/5 in silico tools predict a damaging outcome, and has a low prevalence in European controls (EVS: 2/8576 chrs and ExAC: 25/72,294 chrs). Though the observed allele frequency in general population is not higher than the maximal expected allele frequency for a BRCA2 pathogenic variant (1/1333) the presence of this variant in controls indicates that this variant might be a rare polymorphism. More importantly, the variant has been reported to co-occur with other deleterious variants in BRCA2 and BRCA1 (4 independent individuals who carry pathogenic variants in each BRCA1 and BRCA2, reported in UMD and BIC), strong evidence that this variantis benign. In addition, it has also been classified as benign by multiple reputable databases and clinical labs, databases and publications (Easton_2007, Lindor_2012 and Whiley_2014). There are no functional studies reported for the variant to date. Multifactorial probability based model also shows the variant to be benign. Taken together, this variant has been classified as Benign.
Invitae RCV000044548 SCV000072561 benign Hereditary breast and ovarian cancer syndrome 2017-12-29 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000074533 SCV000538493 uncertain significance not specified 2016-03-31 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: 24/65694 European; ClinVar: 3B/LB, 2 VUS
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000587449 SCV000778680 likely benign not provided 2017-10-16 no assertion criteria provided clinical testing
Michigan Medical Genetics Laboratories,University of Michigan RCV000113374 SCV000195987 likely benign Breast-ovarian cancer, familial 2 2014-11-03 criteria provided, single submitter clinical testing

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