ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1545C>G (p.Ser515Arg)

gnomAD frequency: 0.00114  dbSNP: rs150367385
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000194020 SCV000196867 benign not specified 2017-10-30 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.
Eurofins Ntd Llc (ga) RCV000194020 SCV000226493 likely benign not specified 2015-09-17 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000194020 SCV000248584 likely benign not specified 2015-09-18 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000175066 SCV000280635 likely benign not provided 2016-05-06 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
PreventionGenetics, part of Exact Sciences RCV000194020 SCV000311736 likely benign not specified criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001086216 SCV000649882 likely benign Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2024-02-01 criteria provided, single submitter clinical testing
Mendelics RCV000988264 SCV001137919 benign Autosomal recessive limb-girdle muscular dystrophy type 2K 2019-05-28 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000680152 SCV001368299 benign Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2019-03-26 criteria provided, single submitter clinical testing This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2.
CeGaT Center for Human Genetics Tuebingen RCV000175066 SCV001371091 likely benign not provided 2024-10-01 criteria provided, single submitter clinical testing POMT1: BS1
Athena Diagnostics RCV000194020 SCV001880377 likely benign not specified 2024-02-08 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000194020 SCV002103837 benign not specified 2022-02-25 criteria provided, single submitter clinical testing Variant summary: POMT1 c.1611C>G (p.Ser537Arg) 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 0.0016 in 155618 control chromosomes in the gnomAD database, including 1 homozygote. The observed variant frequency is approximately 2.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in POMT1 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive phenotype (0.00072), strongly suggesting that the variant is benign. Although listed in the literature, to our knowledge, no penetrant association of c.1611C>G in individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive and no experimental evidence demonstrating its impact on protein function have been reported. Ten clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and a predominant consensus as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Baylor Genetics RCV000680152 SCV000807617 likely benign Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 no assertion criteria provided clinical testing

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