The c.2799+2C>A variant alters the consensus donor splice site of intron 19, the final intron of GAA. Assuming that this results in skipping of exon 19, an in frame deletion of ~5% of the length of GAA would occur. Based on the specifications of the ClinGen LSD VCEP, PVS1_Moderate can be applied. The variant is absent in gnomAD v2.1.1, meeting PM2. Of note, the first two nucleotides of intron 19 are GC, rather than the typical GT, and therefore computational splice site predictors may not be reliable in assessing the impact of this variant. To our knowledge, this variant has not been reported in the literature in individuals with Pompe disease, and the results of experimental studies to investigate its impact on splicing are not available. There is a ClinVar entry for the variant (Variant ID: 556975, 1 star review status) with one submitter classifying the variant as likely pathogenic. 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: PVS1_Moderate, PM2.