ACMG/AMP classifier

Null variant in LOF gene

Null variant (nonsense, frameshift, canonical splice site ±1/2, initiation codon, exon deletion) in gene where LOF is known mechanism.

Same amino acid change as established pathogenic

Same amino acid change as established pathogenic variant, regardless of nucleotide change.

De novo (confirmed with parental testing)

De novo variant (confirmed maternity and paternity) in a patient with disease and no family history.

Well-established functional studies — damaging

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Variant prevalence in affected >> controls

Prevalence of variant in affected individuals significantly increased compared with controls.

Mutational hot spot / well-established functional domain

Located in a mutational hot spot or well-established functional domain (without benign variation).

Absent/extremely rare in population databases

Absent from controls or extremely low AF in gnomAD (PopMax AF < disease-specific threshold).

In trans with pathogenic variant (recessive)

For recessive disorders: variant detected in trans with a known pathogenic variant.

Protein length change (in-frame indel)

Protein length changes due to in-frame indels or stop-loss variants in non-repeat regions, or stop-loss variants.

Novel missense at same codon as established pathogenic

Novel missense change at same position as established pathogenic missense variant (different amino acid).

Assumed de novo (parentage not confirmed)

Assumed de novo, without confirmation of parentage (PS2 strength reduced due to unconfirmed parentage).

Cosegregation in multiple affected family members

Cosegregation with disease in multiple affected family members in a gene definitively known to cause disease.

Missense in gene with low benign missense rate

Missense variant in gene where missense variants are a common mechanism AND benign missense variation rare.

Computational evidence supports damaging effect

Multiple lines of computational evidence (conservation, splicing, functional prediction) support damaging effect.

Phenotype highly specific for this gene

Patient's phenotype or family history highly specific for a single-gene disorder with established gene association.

Reputable source reports variant as pathogenic

Reputable source recently classified variant as pathogenic but evidence not available to the evaluating lab.

Allele frequency > 5% in population databases

Allele frequency > 5% in Exome Sequencing Project, 1000 Genomes Project, or gnomAD (stand-alone benign).

Allele frequency greater than expected for disorder

Allele frequency greater than expected for the disorder (below BA1 threshold but inconsistent with disease prevalence).

Observed in healthy adults (fully penetrant condition)

Observed in a healthy adult individual for a fully penetrant dominant, recessive, or X-linked condition with adult onset.

Functional studies — no damaging effect

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Lack of segregation in affected family members

Lack of segregation in affected members of a family in a gene definitively known to cause disease.

Missense in gene where only LOF causes disease

Missense variant in gene where only truncating variants are known to cause disease.

In trans with pathogenic variant in dominant gene / in cis with pathogenic in recessive

Observed in trans with a pathogenic variant for a fully penetrant AD disorder OR in cis with a pathogenic variant in an AR gene.

In-frame indel in repeat region without known function

In-frame deletions/insertions in a repetitive region without a known function.

Computational evidence supports benign effect

Multiple lines of computational evidence suggest benign impact on gene/gene product.

Variant found in case with alternate molecular explanation

Variant found in a case with an alternate molecular basis for disease.

Reputable source reports variant as benign

Reputable source recently classified variant as benign but evidence not available to evaluating lab.

Synonymous variant — no predicted splicing impact

Synonymous variant predicted to have no impact on splicing.