ClinVar Miner

Submissions for variant NM_000170.2(GLDC):c.2380G>A (p.Ala794Thr) (rs141933811)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000243892 SCV000302843 benign not specified criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000515011 SCV000610579 likely benign not provided 2017-05-08 criteria provided, single submitter clinical testing
Invitae RCV001079808 SCV000636384 benign Non-ketotic hyperglycinemia 2020-12-05 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000515011 SCV000842222 benign not provided 2018-03-30 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000515011 SCV001155600 likely benign not provided 2019-08-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001079808 SCV001328172 benign Non-ketotic hyperglycinemia 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 RCV000243892 SCV001482255 benign not specified 2021-02-22 criteria provided, single submitter clinical testing Variant summary: GLDC c.2380G>A (p.Ala794Thr) results in a non-conservative amino acid change in 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 0.0069 in 251474 control chromosomes, predominantly at a frequency of 0.009 within the Non-Finnish European subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 2.9 fold of the estimated maximal expected allele frequency for a pathogenic variant in GLDC causing Glycine Encephalopathy (Non-Ketotic Hyperglycinemia) phenotype (0.0031), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. No occurrence of c.2380G>A in individuals affected with Glycine Encephalopathy (Non-Ketotic Hyperglycinemia) and no experimental evidence demonstrating its impact on protein function was ascertained in the context of this evaluation. 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 (n=3)/likely benign (n=2). Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV000515011 SCV001892938 benign not provided 2018-09-18 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000515011 SCV001932093 likely benign not provided no assertion criteria provided clinical testing

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