ClinVar Miner

Submissions for variant NM_000158.4(GBE1):c.2017G>A (p.Ala673Thr)

gnomAD frequency: 0.00456  dbSNP: rs193074572
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224407 SCV000281238 benign not provided 2015-02-10 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000245211 SCV000302746 benign not specified 2016-02-17 criteria provided, single submitter clinical testing
GeneDx RCV000224407 SCV000519972 benign not provided 2020-05-20 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26670585, 31862442)
Invitae RCV001082988 SCV000626775 benign Glycogen storage disease, type IV; Glycogen storage disease IV, classic hepatic 2020-12-08 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000224407 SCV000693111 likely benign not provided 2022-07-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001151097 SCV001312200 benign Adult polyglucosan body disease 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.
Illumina Laboratory Services,Illumina RCV001151098 SCV001312201 benign Glycogen storage disease, type IV 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000245211 SCV002555742 benign not specified 2022-06-08 criteria provided, single submitter clinical testing Variant summary: GBE1 c.2017G>A (p.Ala673Thr) results in a non-conservative amino acid change located in the Alpha-amylase/branching enzyme, C-terminal all beta domain (IPR006048) of 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 0.005 in 277576 control chromosomes (gnomAD), predominantly at a frequency of 0.0083 within the Non-Finnish European subpopulation in the gnomAD database, including 6 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 6 fold of the estimated maximal expected allele frequency for a pathogenic variant in GBE1 causing Glycogen Storage Disease, Type IV (0.0013), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. Six ClinVar submitters have assessed the variant since 2014: one classified the variant as likely benign, and five as benign. Based on the evidence outlined above, the variant was classified as benign.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000224407 SCV001978226 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000224407 SCV001979002 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000224407 SCV002036811 likely benign not provided no assertion criteria provided clinical testing

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