The NM_000152.5:c.-32-1G>C variant in GAA alters the canonical acceptor splice site of intron 2 and is predicted cause skipping of exon 2, resulting in an in frame deletion that removes ~19% of the primary amino acid sequence of GAA. Exon 2 contains the start methionine and signal sequence for GAA (amino acids 1-27; https://www.uniprot.org/uniprot/P10253). Another variant in the same region, c.-32-13T>G, is one of the most common known pathogenic variants in GAA and results in leaky skipping of exon 2. Deletion of exon 2 causes complete loss of enzyme activity when expressed in heterologous cells (PMIDs 7881425, 7717400). PVS1 was applied, based on the specifications of the ClinGen Lysosomal Diseases VCEP. The variant is absent in gnomAD v2.1.1, meeting PM2_Supporting. This variant was reported in a French patient with late-onset Pompe disease (PMID 30155607). No additional details regarding enzyme activity, or other variant(s) found in the case were provided, and therefore neither PM3 nor PP4 were applied. There is a ClinVar entry for this variant (Variation ID: 557429). In summary, this variant meets the criteria to be classified as a Likely Pathogenic for Pompe disease. The classification of this variant has been upgraded from Variant of Uncertain Significance to Likely Pathogenic based on the recommendations of the ClinGen Sequence Variant Interpretation Working Group, that a variant meeting PVS1 and PM2_Supporting is classified as Likely Pathogenic (https://clinicalgenome.org/site/assets/files/5182/pm2_-_svi_recommendation_-_approved_sept2020.pdf ) GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): PVS1, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases VCEP on May 26, 2023).