ClinVar Miner

Submissions for variant NM_004006.3(DMD):c.5010G>T (p.Trp1670Cys)

gnomAD frequency: 0.00032  dbSNP: rs727503828
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000723857 SCV000202311 uncertain significance not provided 2017-12-29 criteria provided, single submitter clinical testing
GeneDx RCV000723857 SCV000235871 likely benign not provided 2019-03-28 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 30564623, 14695533)
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000212486 SCV000271666 uncertain significance not specified 2015-09-16 criteria provided, single submitter clinical testing The p.Trp1670Cys variant in DMD has been identified in one individual with DMD ( Hofstra 2004). It has also been identified in 23/47847 European chromosomes, inc luding 4 hemizygotes, by the Exome Aggregation Consortium (ExAC, http://exac.br oadinstitute.org; dbSNP rs727503828). Computational prediction tools and conserv ation analysis suggest that this variant may impact the protein, though this inf ormation is not predictive enough to determine pathogenicity. In summary, the cl inical significance of the p.Trp1670Cys variant is uncertain.
Invitae RCV001088504 SCV000625912 benign Duchenne muscular dystrophy 2024-01-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV002336308 SCV002640773 likely benign Cardiovascular phenotype 2018-03-02 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000212486 SCV002819398 likely benign not specified 2022-12-09 criteria provided, single submitter clinical testing Variant summary: DMD c.5010G>T (p.Trp1670Cys) results in a non-conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00021 in 183125 control chromosomes in the gnomAD database with 9 hemizygotes. The observed variant frequency is approximately 19 fold of the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Dystrophinopathies phenotype (1.1e-05), strongly suggesting that the variant is benign. c.5010G>T has been reported in at-least one gender unspecified individual affected with DMD and a non-informative genotype (example: Hofstra_2004). This report does not provide unequivocal conclusions about association of the variant with Dystrophinopathies. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=2) and benign /likely benign (n=3). Based on the evidence outlined above, the variant was classified as likely benign.
CeGaT Center for Human Genetics Tuebingen RCV000723857 SCV004164732 likely benign not provided 2022-05-01 criteria provided, single submitter clinical testing DMD: BS2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000723857 SCV001741022 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000723857 SCV001932643 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000723857 SCV001976001 likely benign not provided no assertion criteria provided clinical testing

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