ClinVar Miner

Submissions for variant NM_000117.3(EMD):c.399+18C>T

gnomAD frequency: 0.00199  dbSNP: rs182540760
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124887 SCV000168327 benign not specified 2014-04-24 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000124887 SCV001572375 benign not specified 2021-04-05 criteria provided, single submitter clinical testing Variant summary: EMD c.399+18C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 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 0.0022 in 181632 control chromosomes, predominantly at a frequency of 0.013 within the Latino subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 13 fold of the estimated maximal expected allele frequency for a pathogenic variant in EMD causing Emery-Dreifuss Muscular Dystrophy phenotype (0.001), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. To our knowledge, no occurrence of c.399+18C>T in individuals affected with Emery-Dreifuss Muscular Dystrophy and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV002055529 SCV002326285 benign X-linked Emery-Dreifuss muscular dystrophy 2024-01-31 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002055529 SCV002803585 likely benign X-linked Emery-Dreifuss muscular dystrophy 2021-10-18 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001725985 SCV005275119 benign not provided criteria provided, single submitter not provided
Clinical Genetics, Academic Medical Center RCV000124887 SCV001921708 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001725985 SCV001964874 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001725985 SCV001978025 likely benign not provided no assertion criteria provided clinical testing

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