Reevaluating the Mutation Classification in Genetic Studies of Bradycardia Using ACMG/AMP Variant Classification Framework

Table 1

Pathogenic and benign criterion based on ACMG/AMP classification framework.

Rule	Category	Rule description
Evidence of pathogenic
Very strong	PVS1	Null variants which caused loss of function are known to be the mechanism of diseases.
Strong	PS1	Different nucleotide change caused same amino acid change with known pathogenic variants.
	PS2	De novo (confirmed maternity and paternity) in a patient with no family history and diseases.
	PS3	Functional studies supported the effect of related pathogenic variants.
	PS4	Variants’ prevalence significantly increased in affected individuals than controls.
Moderate	PM1	Mutation happened in hot spot and known function domain.
	PM2	Absent (or extremely low) in large population studies.
	PM3	With recessive disease, detected in trans with pathogenic variants.
	PM4	Variants (in-frame deletions/insertions in a nonrepeat region or stop-loss variants) lead to changes in protein length.
	PM5	Different missense changes at known pathogenic amino acid residue.
	PM6	De novo (without confirmation of maternity and paternity).
Supporting	PP1	Variants known to be the causes affected multiple family members.
	PP2	Missense variants in a gene that have a low rate of benign missense variation are common mechanism of disease.
	PP3	Multiple lines of computational evidence support a deleterious effect on the gene or gene products.
	PP4	Phenotype specific for disease with single genetic etiology.
	PP5	Reputable source reports variants as pathogenic.
Evidence of benign
Stand-alone	BA1	Allele frequency is >0.5% base on population database.
Strong	BS1	Allele frequency is greater than expected for disorder.
	BS2	Recessive heredity being observed in healthy adult.
	BS3	Functional studies show no pathogenic effect.
	BS4	Without segregation.
Supporting	BP1	Missense variant in gene where only loss of function is pathogenic.
	BP2	Observed in genes with overlapping function without increased disease severity or observed in cis with a pathogenic variant.
	BP3	Variants (in-frame deletions/insertions in a nonrepeat region or stop-loss variants) lead to changes in a repetitive region without known function.
	BP4	Multiple lines of computational evidence suggest no impact on gene or gene product.
	BP5	Variant found in a case with alternate molecular basis for disease.
	BP6	Report as benign.
	BP7	Splicing variant predict an algorithm which predict no impact to the splice consensus sequence.