ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.1040A>G (p.Gln347Arg) (rs55800493)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589778 SCV000883473 likely benign not provided 2017-06-27 criteria provided, single submitter clinical testing The BRCA2 c.1040A>G; p.Gln347Arg variant (rs55800493) is reported as a likely benign or benign variant in ClinVar (Variation ID: 51060), and observed in general population databases with overall allele frequencies of 0.24 percent (12/5008 alleles, 1000 Genomes Project), 0.13 percent (17/12996 alleles, Exome Variant Server), and 0.038 percent (103/274396 alleles, Genome Aggregation Database) with an increased frequency of 0.4 percent in the African population. The glutamine at codon 347 is weakly conserved and computational algorithms (SIFT, PolyPhen2, MutationTaster, Prior Probabilities) predict this variant to be tolerated. Based on the above information, this variant is considered likely benign. REFERENCES Link to ClinVar database for p.Gln347Arg: https://www.ncbi.nlm.nih.gov/clinvar/variation/51060/
Ambry Genetics RCV000131469 SCV000186456 likely benign Hereditary cancer-predisposing syndrome 2017-10-11 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Other data supporting benign classification,Subpopulation frequency in support of benign classification
Breast Cancer Information Core (BIC) (BRCA2) RCV000077248 SCV000145810 uncertain significance Breast-ovarian cancer, familial 2 2004-02-20 no assertion criteria provided clinical testing
Color RCV000131469 SCV000902747 benign Hereditary cancer-predisposing syndrome 2016-01-05 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000077248 SCV000744400 likely benign Breast-ovarian cancer, familial 2 2015-09-21 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000173638 SCV000591726 likely benign not specified 2016-02-10 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000173638 SCV000224769 likely benign not specified 2015-01-08 criteria provided, single submitter clinical testing
GeneDx RCV000173638 SCV000210554 likely benign not specified 2018-02-23 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.
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam RCV000077248 SCV000745675 likely benign Breast-ovarian cancer, familial 2 2017-05-21 no assertion criteria provided clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589778 SCV000694503 likely benign not provided 2016-04-11 criteria provided, single submitter clinical testing Variant summary: The c.1040A>G variant affects a non-conserved nucleotide, resulting in amino acid change from Gln to Arg. 4/5 in-silico tools predict this variant to be benign. This variant is found in 47/120376 control chromosomes at a frequency of 0.0003904, however is present at 10-fold higher frequency in the African population (0.004533 in ExAC), which exceeds the maximum expected allele frequency for a pathogenic variant in BRCA2 (0.0007503). This suggests that this variant is a benign polymorphism in populations of African origin. This variant has been reported in BrC or OvC patients without evidence for causality. Multiple clinical laboratories classified this variant as benign/likely benign. Taken together, this variant is classified as Likely Benign until additional information becomes available.
Invitae RCV000167809 SCV000071747 benign Hereditary breast and ovarian cancer syndrome 2018-01-05 criteria provided, single submitter clinical testing
PreventionGenetics RCV000589778 SCV000805645 likely benign not provided 2017-05-05 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000173638 SCV000600460 likely benign not specified 2017-02-06 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589778 SCV000887744 likely benign not provided 2018-02-22 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000077248 SCV000109045 likely benign Breast-ovarian cancer, familial 2 2008-05-22 no assertion criteria provided clinical testing

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