ClinVar Miner

Submissions for variant NM_000252.3(MTM1):c.582C>T (p.Leu194=)

gnomAD frequency: 0.00029  dbSNP: rs367912069
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Congenital Myopathies Variant Curation Expert Panel, ClinGen RCV004732475 SCV005367896 benign Centronuclear myopathy 2024-08-07 reviewed by expert panel curation The variant NM_000252.3(MTM1):c.582C>T is a synonymous (silent) variant (p.Leu194=). The filtering allele frequency in gnomAD v4.1.0 is 0.002821 (112/33731 alleles, 2 homozygote, 36 hemizygotes) for the East Asian population, which is higher than the ClinGen congenital myopathy MTM1 threshold (≥0.000016) for BA1, and therefore meets this criterion (BA1). In addition, SpliceAI predicted no impact on splicing, meeting BP4/BP7 criteria. In summary, the variant meets criteria to be classified as benign. ACMG/AMP criteria met, as specified by the congenital myopathies VCEP: BA1, BP4, BP7 (ClinGen Congenital Myopathies VCEP specifications version 1; 8/7/2024).
GeneDx RCV000433479 SCV000526297 likely benign not specified 2017-05-26 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000541166 SCV000634493 benign Severe X-linked myotubular myopathy 2025-01-23 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000433479 SCV005621185 benign not specified 2024-01-11 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004533040 SCV004723943 benign MTM1-related disorder 2024-02-19 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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