ClinVar Miner

Submissions for variant NM_004006.3(DMD):c.1869C>T (p.Leu623=) (rs1800267)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000080468 SCV000112370 benign not specified 2014-04-29 criteria provided, single submitter clinical testing
GeneDx RCV000080468 SCV000168168 benign not specified 2014-03-28 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000080468 SCV000268947 benign not specified 2015-01-13 criteria provided, single submitter clinical testing p.Leu623Leu in exon 16 of DMD: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 10.9% (418/3833) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs. gs.washington.edu/EVS/; dbSNP rs1800267).
PreventionGenetics,PreventionGenetics RCV000080468 SCV000309924 benign not specified criteria provided, single submitter clinical testing
Ambry Genetics RCV000245650 SCV000318586 benign Cardiovascular phenotype 2015-10-20 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
Illumina Clinical Services Laboratory,Illumina RCV000285906 SCV000482273 benign Dilated cardiomyopathy 3B 2018-01-13 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 RCV000470353 SCV000560810 benign Duchenne muscular dystrophy 2019-12-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000080468 SCV000603341 benign not specified 2018-08-05 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000711449 SCV000841816 benign not provided 2017-10-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000080468 SCV000919264 benign not specified 2018-07-13 criteria provided, single submitter clinical testing Variant summary: DMD c.1869C>T alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.011 in 200065 control chromosomes, predominantly at a frequency of 0.11 within the African subpopulation in the gnomAD database, including 93 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 9.84 fold of the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Dystrophiopathies phenotype (0.011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.1869C>T in individuals affected with Dystrophiopathies 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/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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