The highest population minor allele frequency in gnomAD v2.1.1 for c.1288G>A (p.Glu430Lys) is 0.00043 in the African population, meeting the ClinGen LSD VCEP’s PM2 allele frequency threshold (<0.001). The score for the in silico meta-predictor REVEL, 0.577, is below the ClinGen LSD VCEP’s threshold for PP3 (>0.7) and above the threshold for BP4 (<0.5), and therefore neither can be applied. To our knowledge, this variant has not been reported in the literature in individuals with Pompe disease, and the results of functional studies are not available. However, there is a ClinVar entry for this variant (Variation ID: 501777; 2 star review status) with two submitters classifying this variant as uncertain significance. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PM2.