ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.858+17_858+23del

dbSNP: rs1555599723
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001591127 SCV000569348 benign not provided 2018-05-09 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001271973 SCV001471592 benign Glycogen storage disease, type II 2022-03-07 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001824798 SCV002074255 benign not specified 2022-01-14 criteria provided, single submitter clinical testing Variant summary: GAA c.858+17_858+23delCGGGCGG alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0015 in 274012 control chromosomes, predominantly at a frequency of 0.016 within the African or African-American subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 4 fold of the estimated maximal expected allele frequency for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) phenotype (0.0042), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.858+17_858+23delCGGGCGG in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submitters (evaluation after 2014) cited the variant as benign (n=2) and likely benign (n=2). Based on the evidence outlined above, the variant was classified as benign.
Natera, Inc. RCV001271973 SCV001453598 likely benign Glycogen storage disease, type II 2020-09-16 no assertion criteria provided clinical testing
GeneDx RCV001591127 SCV001826669 likely benign not provided 2018-09-04 flagged submission clinical testing

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