ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.112A>G (p.Thr38Ala) (rs35278779)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000241781 SCV000305373 likely benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000241781 SCV000336088 benign not specified 2015-10-02 criteria provided, single submitter clinical testing
GeneDx RCV000241781 SCV000521271 benign not specified 2016-03-09 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 RCV001082613 SCV000626664 benign Glycogen storage disease type III 2020-12-04 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000241781 SCV000916427 benign not specified 2018-09-17 criteria provided, single submitter clinical testing Variant summary: AGL c.112A>G (p.Thr38Ala) results in a non-conservative amino acid change located in the Eukaryotic glycogen debranching enzyme, N-terminal domain of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0049 in 277070 control chromosomes, predominantly at a frequency of 0.05 within the African subpopulation in the gnomAD database, including 17 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 22-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in AGL causing Glycogen Storage Disease Type III phenotype (0.0023), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV001082613 SCV001256665 benign Glycogen storage disease type III 2019-03-07 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000675317 SCV000800982 benign not provided 2017-10-16 no assertion criteria provided clinical testing
Natera, Inc. RCV001082613 SCV001454494 benign Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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