ClinVar Miner

Submissions for variant NM_000152.3(GAA):c.2065G>A (p.Glu689Lys)

gnomAD frequency: 0.04051  dbSNP: rs1800309
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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000078165 SCV000110003 benign not specified 2012-09-10 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000078165 SCV000302673 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000383641 SCV000407290 benign Glycogen storage disease, type II 2018-03-06 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Phosphorus, Inc. RCV000383641 SCV000679831 benign Glycogen storage disease, type II 2017-08-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000383641 SCV000752099 other Glycogen storage disease, type II 2019-01-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000383641 SCV001158934 benign Glycogen storage disease, type II 2023-11-29 criteria provided, single submitter clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV000383641 SCV001422940 benign Glycogen storage disease, type II 2020-01-22 criteria provided, single submitter curation The p.Glu689Lys variant in GAA has been reported as a benign and likely benign variant for Glycogen Storage Disease II in ClinVar (Variation ID: 4030). This variant has been identified in 5.490% (13805/251476) of chromosomes, including 757 homozygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs1800309). This variant has been seen in the general population at a frequency high enough to rule out a pathogenic role. It is a known pseudodeficiency allele that causes false-positive results in GAA deficiency enzyme assays (PMID: 20080426, 18301443). In summary, this variant meets criteria to be classified as benign for Glycogen Storage Disease II in an autosomal recessive manner based on its frequency in the general population. ACMG/AMP Criteria applied: BA1 (Richards 2015).
Genome-Nilou Lab RCV000383641 SCV001738047 benign Glycogen storage disease, type II 2021-06-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV002415397 SCV002725156 benign Cardiovascular phenotype 2018-12-11 criteria provided, single submitter clinical testing This alteration is classified as 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.
Breakthrough Genomics, Breakthrough Genomics RCV000675237 SCV005248758 benign not provided criteria provided, single submitter not provided
OMIM RCV000004245 SCV000024411 pathogenic Acid alpha-glucosidase, allele 4 1996-09-01 flagged submission literature only
Genetic Services Laboratory, University of Chicago RCV000078165 SCV000151253 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Mayo Clinic Laboratories, Mayo Clinic RCV000675237 SCV000800883 benign not provided 2015-12-16 no assertion criteria provided clinical testing
GenomeConnect - Invitae Patient Insights Network RCV000675237 SCV001749932 not provided not provided no assertion provided phenotyping only Variant reported in multiple Invitae PIN participants. Variant interpreted as Benign (Pseudo deficiency allele) most recently on 9/29/2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000078165 SCV001928177 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000078165 SCV001972654 benign not specified no assertion criteria provided clinical testing

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