ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.551C>T (p.Thr184Met)

gnomAD frequency: 0.01026  dbSNP: rs35889956
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000116544 SCV000230021 benign not specified 2016-07-28 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000116544 SCV000301893 likely benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000116544 SCV000520878 benign not specified 2016-05-19 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.
Invitae RCV000547941 SCV000645505 benign Autosomal recessive limb-girdle muscular dystrophy type 2A 2021-12-18 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000547941 SCV001275824 benign Autosomal recessive limb-girdle muscular dystrophy type 2A 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Athena Diagnostics Inc RCV001288906 SCV001476316 likely benign not provided 2020-05-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000116544 SCV002104106 benign not specified 2022-02-18 criteria provided, single submitter clinical testing Variant summary: CAPN3 c.551C>T (p.Thr184Met) results in a non-conservative amino acid change located in the Peptidase C2, calpain, catalytic domain (IPR001300) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0024 in 251442 control chromosomes, predominantly at a frequency of 0.035 within the African or African-American subpopulation in the gnomAD database, including 13 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 11 fold of the estimated maximal expected allele frequency for a pathogenic variant in CAPN3 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive phenotype (0.0032), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Six ClinVar submitters have assessed the variant since 2014: five classified the variant as benign and one as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Genetic Services Laboratory,University of Chicago RCV000116544 SCV000150499 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.
Natera, Inc. RCV000547941 SCV001461308 benign Autosomal recessive limb-girdle muscular dystrophy type 2A 2020-09-16 no assertion criteria provided clinical testing

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