Submissions for variant NM_001077365.2(POMT1):c.699+52C>T

gnomAD frequency: 0.12205  dbSNP: rs3887873

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000081492	SCV000113423	benign	not specified	2012-07-24	criteria provided, single submitter	clinical testing
GeneDx	RCV000081492	SCV000171151	benign	not specified	2013-12-19	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000081492	SCV000269710	benign	not specified	2015-04-28	criteria provided, single submitter	clinical testing	p.Gln251Trp in exon 8 of POMT1: This variant is not expected to have clinical si gnificance because it has been identified in at least 8.8% (10687/121366) of chr omosomes from multiple diverse populations by the Exome Aggregation Consortium ( ExAC, http://exac.broadinstitute.org).
PreventionGenetics, part of Exact Sciences	RCV000081492	SCV000311758	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000326785	SCV000477654	likely benign	Autosomal recessive limb-girdle muscular dystrophy type 2K	2017-04-27	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Athena Diagnostics	RCV000576730	SCV000677417	benign	not provided	2017-04-14	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001789139	SCV002031744	benign	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1	2021-10-25	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001789138	SCV002031745	benign	Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1	2021-10-25	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000326785	SCV002031746	benign	Autosomal recessive limb-girdle muscular dystrophy type 2K	2021-10-25	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000081492	SCV002051256	benign	not specified	2021-12-19	criteria provided, single submitter	clinical testing	Variant summary: POMT1 c.751C>T (p.Gln251X) results in a premature termination codon. The variant allele was found at a frequency of 0.1 in 251118 control chromosomes in the gnomAD database, including 1602 homozygotes. The observed variant frequency is approximately 140.65 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. Five 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 benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Breakthrough Genomics, Breakthrough Genomics	RCV000576730	SCV005225915	likely benign	not provided		criteria provided, single submitter	not provided
Genetic Services Laboratory, University of Chicago	RCV000081492	SCV000152359	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Clinical Genetics, Academic Medical Center	RCV000576730	SCV001922441	likely benign	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000081492	SCV001957260	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000081492	SCV001968056	benign	not specified		no assertion criteria provided	clinical testing