Table 1:

Utilization of ACMG criteria and knowledgebase in PathoMAN variant curation

Category	ACMG criteria	Utilization of ACMG criteria in PathoMAN’s variant classification
literature and other sources	PVS1	Tier 1 variants (Frameshift, truncating, essential splice and initiation codon) in curated list of OG and TSG and not in last exon
public databases		Missense variant (hgvs protein change) in ClinVar with review status >= 2 irrespective of the genomic alternative allele
de novo data	PS2	User Input
public databases; functional data	PS3	Variant in list of pathogenic variants knowledgebase aggregated from literature with functional evidence, public database with loss of function reports, Tier 1 variants in ClinVar reported with review status >=2 and missense variants reported by ENIGMA
population frequency data	PS4	Fisher’s case-control test odds ratio > 3 and Pval < 0.05 against ExAC-noTCGA and gnomAD population of interest (Applies to variants with BA1, BS1, BS2 and PM2 equal to 0)
public databases	PM1	Amino acid residue in protein’s domain or residue for signalling or protein-protein interaction or in active site from Uniprot
population frequency data	PM2	Variant absent from ExAC-noTCGA or gnomAD
allelic/genotypic data	PM3	Not used in the current version
public databases	PM4	Inframe ins/del or stop loss in a non-repetitive region from UCSC genome browser
public databases	PM5	Missense variant in ClinVar with review status >=2 irrespective of the alternative amino acid change at the same position as that of the reported pathogenic variant in clinvar
de novo data	PM6	User Input
segregation data	PP1	User Input
public databases	PP2	Variant in gene with significant pathogenic missense burden in ClinVar
genomic annotation and computational predictive data	PP3	in-silico predictors agree on pathogenicity or deleteriousness of the variant
Other (disease specific)	PP4	Not used in the current version
public databases	PP5	Variant in ClinVar with review status <2 and pathogenic without conflicts
population frequency data	BA1	Variant seen in ExAC-noTCGA or gnomAD with AF > 5%
population frequency data	BS1	Variant seen in ExAC-noTCGA or gnomAD with AF between 1%–5%
population frequency data	BS2	Variant seen in ExAC-noTCGA or gnomAD general population in homozygous form
public databases; functional data	BS3	Variant in list of benign variants knowledgebase aggregated from literature with functional evidence, public database with loss of function reports, Tier 1 variants in ClinVar reported with review status >=2 and missense variants reported by ENIGMA
de novo data	BS4	User Input
public databases	BP1	Variant in gene with significant benign missense burden in ClinVar
allelic/genotypic data	BP2	Not used in the current version
public databases	BP3	Inframe ins/del or stop loss in a repetitive region from UCSC genome browser
genomic annotation and computational predictive data	BP4	in-silico predictors agree on benignity or tolerance of the variant
Other (disease specific)	BP5	Not used in the current version
public databases	BP6	Variant in ClinVar with review status <2 and benign without conflicts
genomic annotation and computational predictive data	BP7	synonymous variant with dbscSNV adaptive boosting and random forest score < 0.6