ClinVar Miner

Submissions for variant NM_004006.2(DMD):c.4529A>G (p.Lys1510Arg) (rs72468638)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000080622 SCV000112524 benign not specified 2016-01-08 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000372007 SCV000482252 benign Dilated cardiomyopathy 3B 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV001084663 SCV000560834 benign Duchenne muscular dystrophy 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000620501 SCV000735622 benign Cardiovascular phenotype 2016-11-22 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute RCV000845340 SCV000987386 likely benign not provided criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000080622 SCV001338380 benign not specified 2020-02-21 criteria provided, single submitter clinical testing Variant summary: DMD c.4529A>G (p.Lys1510Arg) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0057 in 181352 control chromosomes in the gnomAD database (exomes dataset), including 13 homozygotes, and 319 hemizygotes. The observed variant frequency is approximately 500 fold of the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Dystrophinopathy phenotype (1.1e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.4529A>G in individuals affected with Dystrophinopathies and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign (3x) / likely benign (2x). Based on the evidence outlined above, the variant was classified as benign.

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