ClinVar Miner

Submissions for variant NM_000170.2(GLDC):c.1545G>A (p.Arg515=) (rs121964976)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000248102 SCV000613526 benign not specified 2017-06-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000248102 SCV000919472 benign not specified 2018-09-27 criteria provided, single submitter clinical testing Variant summary: GLDC c.1545G>A alters a non-conserved nucleotide resulting in a synonymous change. The variant allele was found at a frequency of 0.022 in 277184 control chromosomes in the gnomAD database, including 99 homozygotes. The observed variant frequency is approximately 7-fold above 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 benign. c.1545G>A has been reported in the literature in an individual affected with Glycine Encephalopathy (Non-Ketotic Hyperglycinemia), though this patient had two pathogenic mutations in trans, supporting a benign impact of the variant. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and both classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV000530402 SCV000636357 benign Non-ketotic hyperglycinemia 2017-08-08 criteria provided, single submitter clinical testing
PreventionGenetics RCV000248102 SCV000302841 benign not specified criteria provided, single submitter clinical testing
SingHealth Duke-NUS Institute of Precision Medicine RCV000530402 SCV000853163 uncertain significance Non-ketotic hyperglycinemia 2017-06-07 no assertion criteria provided curation

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