The NM_000152.5:c.2161dup (p.Glu721GlyfsTer16) variant in GAA is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 16 out of 20, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). One individual with this variant and Pompe disease has been reported in the literature, but the residual GAA activity and second variant were not provided and therefore PP4 cannot be assessed (PMID: 18425781). Another individual with "p.E721Rfs", identified by newborn screening had been reported (PMIDs 28196920, 29095812) but the cDNA change was not provided. There is a ClinVar entry for this variant (Variation ID: 550277). This variant meets the criteria to be classified as 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 ). The classification was first approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on September 7, 2021. Since then, the data for this variant have been re-evaluated - no new data were identified. The classification of likely pathogenic was reapproved on April 5, 2024. GAA-specific ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert Panel (Specifications Version 2.0): PVS1, PM2_Supporting.