The c.1888+5G>T variant alters the donor splice site consensus sequence of intron 13. In silico splicing prediction programs, Human Splicing Finder and MaxEntScan, suggest that the variant disrupts normal splicing; the scores are decreased by 12.74% and 55.42% respectively, allowing PP3 to be applied. The highest population minor allele frequency for this variant in gnomAD is 0.00006024 in the Latino population, meeting the ClinGen LSD VCEP’s threshold for PM2. To our knowledge, this variant has not been reported in the literature in individuals with Pompe disease, and results of functional or splicing studies are not available. However, there is a ClinVar entry for this variant (Variation ID 283971) in which one of two submitters identified the variant in a patient with Pompe disease; no further clinical or laboratory results are available. In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PM2, PP3.