ClinVar Miner

Submissions for variant NM_000117.2(EMD):c.466G>A (p.Gly156Ser) (rs144594695)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000183440 SCV000235900 likely benign not specified 2017-08-02 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.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000183440 SCV000337756 likely benign not specified 2015-12-08 criteria provided, single submitter clinical testing
Invitae RCV000467850 SCV000560795 likely benign Emery-Dreifuss muscular dystrophy 1, X-linked 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000183440 SCV000917316 likely benign not specified 2018-11-19 criteria provided, single submitter clinical testing Variant summary: EMD c.466G>A (p.Gly156Ser) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00032 in 199875 control chromosomes, including 20 hemizygotes, in the gnomAD database. The variant was predominantly observed within the African subpopulation, at a frequency of 0.0032 (including 18 hemizygotes), and although this frequency is somewhat lower than expected for a pathogenic variant in EMD causing Cardiomyopathy (0.0032 vs 0.0071), the large number of hemizygotes among the controls suggests that the variant still might be a benign polymorphism. To our knowledge, no occurrence of c.466G>A in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Three 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 likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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