ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2800-15CT[3] (rs770227589)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000732109 SCV000716170 likely benign not provided 2020-09-02 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000732109 SCV000860015 uncertain significance not provided 2018-03-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000608615 SCV001363617 uncertain significance not specified 2019-04-11 criteria provided, single submitter clinical testing Variant summary: GAA c.2800-9_2800-8delCT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/5 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 0.00017 in 277090 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.2800-9_2800-8delCT in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (1xlikely benign, 1xVUS). Based on the evidence outlined above, the variant was classified as uncertain significance.
Nilou-Genome Lab RCV001580525 SCV001810205 uncertain significance Glycogen storage disease, type II 2021-07-22 criteria provided, single submitter clinical testing

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