ClinVar Miner

Submissions for variant NM_004006.2(DMD):c.2575A>T (p.Thr859Ser) (rs187926894)

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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 RCV000176078 SCV000227673 likely benign not specified 2017-07-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV000250419 SCV000319529 likely benign Cardiovascular phenotype 2019-02-19 criteria provided, single submitter clinical testing In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Invitae RCV000463804 SCV000560843 likely benign Duchenne muscular dystrophy 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000176078 SCV000729882 likely benign not specified 2017-11-08 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.
CeGaT Praxis fuer Humangenetik Tuebingen RCV001172201 SCV001335184 likely benign not provided 2020-02-01 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000176078 SCV001362906 likely benign not specified 2019-03-25 criteria provided, single submitter clinical testing Variant summary: DMD c.2575A>T (p.Thr859Ser) results in a conservative amino acid change located in a spectrin repeat (IPR002017) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00011 in 200325 control chromosomes (gnomAD), including 10 hemizygotes. The observed variant frequency is significantly higher than expected for a pathogenic variant in DMD causing Dystrophinopathy phenotype, strongly suggesting that the variant is a benign polymorphism. To our knowledge, no occurrence of c.2575A>T in individuals affected with Dystrophinopathies and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign (3x) and once as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.

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