ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2652G>A (p.Thr884=)

gnomAD frequency: 0.00036  dbSNP: rs143642048
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726336 SCV000343860 uncertain significance not provided 2018-04-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001085559 SCV000626589 likely benign Glycogen storage disease, type II 2024-01-30 criteria provided, single submitter clinical testing
GeneDx RCV000726336 SCV000724068 likely benign not provided 2021-05-05 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001085559 SCV001285669 uncertain significance Glycogen storage disease, type II 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001085559 SCV001422614 likely benign Glycogen storage disease, type II 2020-01-22 criteria provided, single submitter curation The c.2652G>A (p.Thr884=) variant in GAA has not been previously reported in individuals with Glycogen Storage Disease II but has been reported as a VUS by EGL Genetic Diagnostics and a likely benign variant by GeneDx and Invitae in ClinVar (Variation ID: 289488). This variant has been identified in 0.135% (32/23756) of European (Finnish) chromosomes and 0.055% (71/128992) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs143642048). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. However, novel synonymous variants supported by computational evidence without raised suspicion for an impact are likely benign (Richards 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely benign. ACMG/AMP Criteria applied: BP4, BP7 (Richards 2015).
Genome-Nilou Lab RCV001085559 SCV001810199 uncertain significance Glycogen storage disease, type II 2021-07-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV002429231 SCV002743756 likely benign Cardiovascular phenotype 2022-04-01 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Natera, Inc. RCV001085559 SCV002094477 likely benign Glycogen storage disease, type II 2020-02-07 no assertion criteria provided clinical testing

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