ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.258C>A (p.Pro86=)

gnomAD frequency: 0.00147  dbSNP: rs146615896
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000338982 SCV000333379 benign not specified 2015-07-21 criteria provided, single submitter clinical testing
GeneDx RCV000590222 SCV000523296 likely benign not provided 2020-09-08 criteria provided, single submitter clinical testing
Invitae RCV001001756 SCV000626585 benign Glycogen storage disease, type II 2021-12-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590222 SCV000695657 likely benign not provided 2017-02-03 criteria provided, single submitter clinical testing Variant summary: The GAA c.258C>A (p.Pro86Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect binding of an ESE site. These predictions have yet to be confirmed by functional studies. This variant was found in 69/114570 control chromosomes from ExAC, predominantly observed in the African subpopulation at a frequency of 0.006696 (64/9558). This frequency is about 1.6 times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. No homozygotes have been reported in ExAC. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. A clinical diagnostic laboratory in ClinVar has classified this variant as benign. Taken together, this variant is classified as Likely Benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001001756 SCV001159368 benign Glycogen storage disease, type II 2018-12-12 criteria provided, single submitter clinical testing

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