Table 2.

Summary of specifications made to Benign ACMG-AMP criteria codes for the classification of variants in GAA (Version 2).

ACMG/AMP Criterion	ACMG/AMP criterion description	Specification	Strength	Description
BA1	Common in population databases.	Disease-specific	Stand alone	Highest minor allele frequency >0.01 (>1%) in any continental population in gnomAD with >2000 alleles.
BS1	Allele frequency greater than expected for disease.	Disease-specific	Strong	Highest minor allele frequency >0.005 (>0.5%) in any continental population in gnomAD with >2000 alleles.
BS3	Well-established in vitro or in vivo functional studies show no damaging effect on protein function.	Disease-specific, strength	Supporting	>50% activity when the variant is expressed in a heterologous cell type, or >30% activity if there is also evidence of normal synthesis and processing.
BS4	Lack of segregation in affected members of a family.	Not used	N/A	N/A
BP1	Missense variant in gene where only LOF causes disease.	Not used	N/A	N/A
BP2	Observed in cis with a pathogenic variant.	None	Supporting	No changes
BP3	In-frame deletions/insertions in a repetitive region without a known function.	Not used	N/A	N/A
BP4	Multiple lines of computational evidence suggest no impact on gene or gene product.	Gene-specific	Supporting	• REVEL score <0.5 for missense variants. • In-frame deletion or insertion predicted benign by 2 out of 3 tools (e.g. PROVEAN, MutationTaster, and MutPred-InDel). • No predicted impact on splicing by SpliceAI (score <0.2)
BP5	Variant found in a case with an alternate molecular basis for disease.	Not used	N/A	N/A
BP6	Reputable source recently reports the variant as benign but the evidence is not available to the laboratory to perform an independent evaluation.	Not used	N/A	N/A60
BP7	A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.	None	Supporting	No changes