ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.858+7_858+8insAGCGGGC (rs3071247)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel, ClinGen RCV000578107 SCV001443319 benign Glycogen storage disease, type II 2020-05-19 reviewed by expert panel curation The highest continental population minor allele frequency for c.858+7_858+8insAGCGGGC in gnomAD v.2.1.1 is 0.7353 in the European non-Finnish population. This allele frequency is higher than the ClinGen LSD VCEP's BA1 threshold (>0.01), meeting this criterion. Note that the minor allele frequency is even higher in the Ashkenazi Jewish (0.7783) and European Finnish (0.7613) populations. There is a ClinVar entry for this variant (Variation ID: 92489, 2 star review status), with 10 submitters all 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 RCV000078186 SCV000110024 benign not specified 2018-09-04 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000078186 SCV000247443 benign not specified 2015-08-03 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078186 SCV000302699 benign not specified criteria provided, single submitter clinical testing
Phosphorus, Inc. RCV000578107 SCV000679771 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 RCV000588321 SCV000695667 benign not provided 2017-08-21 criteria provided, single submitter clinical testing Variant summary: The GAA c.858+7_858+8insAGCGGGC variant involves insertion of 7 nucleotides in an intronic location, which 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 179851/270478 control chromosomes (3918 homozygotes) at a frequency of 0.6649376, which is approximately 158 times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205). The observed allele frequency indicates the variant of interest is the major allele observed in the general population. In addition, the region is indicated to be highly polymorphic in gnomAD. A publication cites the variant to co-occur in an affected individual that carried two pathogenic variants. Furthermore, multiple clinical diagnostic laboratories classified this variant as benign. Taken together, this variant is classified as benign.
GeneDx RCV000588321 SCV000728468 benign not provided 2018-06-11 criteria provided, single submitter clinical testing
Invitae RCV000578107 SCV000752093 benign Glycogen storage disease, type II 2020-12-04 criteria provided, single submitter clinical testing
GeneDx RCV000588321 SCV001889553 benign not provided 2018-08-28 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000578107 SCV000733726 benign Glycogen storage disease, type II no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000578107 SCV000733727 benign Glycogen storage disease, type II no assertion criteria provided clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000588321 SCV000800867 benign not provided 2015-12-07 no assertion criteria provided clinical testing
Natera, Inc. RCV000578107 SCV001453597 benign Glycogen storage disease, type II 2020-09-16 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000588321 SCV001800190 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000078186 SCV001958325 benign not specified no assertion criteria provided clinical testing

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