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

gnomAD frequency: 0.01527  dbSNP: rs35278779

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000241781	SCV000305373	likely benign	not specified		criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	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	2024-01-31	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 Laboratory Services, 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.
Genome-Nilou Lab	RCV001082613	SCV002055049	benign	Glycogen storage disease type III	2021-07-15	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV001082613	SCV002804181	benign	Glycogen storage disease type III	2022-04-21	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000675317	SCV003800087	likely benign	not provided	2023-11-22	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000675317	SCV003916473	benign	not provided	2023-04-01	criteria provided, single submitter	clinical testing	AGL: BS1, BS2
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