ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.324T>C (p.Cys108=) (rs1800300)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 15
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel, ClinGen RCV000284275 SCV001371707 benign Glycogen storage disease, type II 2020-01-21 reviewed by expert panel curation The highest continental population minor allele frequency for c.324T>C (p.Cys108=) in gnomAD v2.1.1 is 0.81776 in the South Asian population. This is higher than the ClinGen LSD VCEP's BA1 threshold (>0.01), meeting this criterion. There is a ClinVar entry for this variant (Variation ID: 92484, two star review status), with 10 submitters classifying the variant as benign. In summary, this variant meets the criteria to be classified as benign for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: BA1.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000078180 SCV000110018 benign not specified 2018-09-04 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000078180 SCV000151260 benign not specified 2013-08-15 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078180 SCV000302686 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000284275 SCV000407257 benign Glycogen storage disease, type II 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000299885 SCV000483696 benign Primary ciliary dyskinesia 2016-06-14 criteria provided, single submitter clinical testing
Phosphorus, Inc. RCV000284275 SCV000679832 benign Glycogen storage disease, type II 2017-08-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587169 SCV000695661 benign not provided 2017-05-03 criteria provided, single submitter clinical testing Variant summary: The GAA c.324T>C (p.Cys108Cys) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 86202/117014 control chromosomes (32095 homozygotes) at a frequency of 0.7366811, indicating the C allele is the major allele. This frequency is approximately 175 times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant has been classified as benign.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000078180 SCV000711747 benign not specified 2017-05-08 criteria provided, single submitter clinical testing p.Cys108Cys in exon 3 of GAA: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 82% (13463/16390) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac. broadinstitute.org; dbSNP rs1800300).
Invitae RCV000284275 SCV001730023 benign Glycogen storage disease, type II 2020-12-04 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV000284275 SCV001738007 benign Glycogen storage disease, type II 2021-06-10 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000284275 SCV000733721 benign Glycogen storage disease, type II no assertion criteria provided clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000587169 SCV000800857 benign not provided 2015-10-19 no assertion criteria provided clinical testing
Natera, Inc. RCV000284275 SCV001453582 benign Glycogen storage disease, type II 2020-09-16 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000587169 SCV001553818 uncertain significance not provided no assertion criteria provided clinical testing multiple AR variants in same gene - keep for nowAllele frequency is common in at least one population database (frequency: 82.142% in ExAC) based on the frequency threshold of 2.76% for this gene.Variant was observed in a homozygous state in population databases more than expected for disease.10 reputable source/s reports the variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.A synonymous variant not located in a splice region.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.