NGSDiag V2 Variant Classification Guide — Updated ACMG/AMP Criteria
NGSDiag V2 is a French adaptation of the ACMG/AMP 2015 guidelines incorporating ClinGen Sequence Variant Interpretation (SVI) working group recommendations. Key changes from V1: criteria can be applied at modulated strength levels, PP5 and BP6 are removed, PP1 is renamed P1, PP4 is renamed P4, and PM2 is maintained at moderate weight.
PVS1 — Loss of Function (modulated)
PVS1 (Very Strong): Truncating variant, NMD predicted, constitutive exon, LOF is the established disease mechanism.
PVS1_fort (effective weight = Strong): No NMD predicted but loss of >10% of protein or critical domain.
PVS1_moyen (effective weight = Moderate): LOF with uncertain NMD, loss of <10% of protein.
PVS1_faible (effective weight = Supporting): Very minor alternative exon or variant near stop codon with minimal predicted impact.
PS2 — De novo (modulated)
PS2_tfort (effective weight = PVS): Confirmed de novo + highly specific phenotype for the gene-associated disease.
PS2 (Strong): Confirmed de novo, biological parentage confirmed by genetic testing.
PS4 — Disease Prevalence (modulated)
PS4 (Strong): OR > 3 in formal case-control study.
PS4_moyen (effective weight = Moderate): Multiple independent patients, no formal OR calculation.
PS4_faible (effective weight = Supporting): 1–2 patients reported, no formal study.
PM3 — Trans with Pathogenic Variant (modulated)
PM3_fort (effective weight = Strong): Confirmed trans in multiple independent index cases (recessive disease).
PM3 (Moderate): Confirmed trans in a single patient, phase biologically confirmed.
PM3_faible (effective weight = Supporting): Probable trans, phase not biologically confirmed.
PM6 — Presumed De Novo (modulated)
PM6 (Moderate): Clinically de novo, biological parentage not confirmed, full penetrance expected.
PM6_faible (effective weight = Supporting): Presumed de novo + incomplete penetrance or non-specific phenotype.
P1 / PP1 — Co-segregation (modulated, renamed from PP1)
P1_fort (effective weight = Strong): LOD ≥ 3 or ≥ 5 affected tested members carrying the variant.
P1_moyen (effective weight = Moderate): LOD ≥ 2 or ≥ 4 affected members.
P1 / PP1 (Supporting): LOD ≥ 1 or ≥ 3 affected members.
P4 / PP4 — Phenotype Specificity (modulated, renamed from PP4)
P4_moyen (effective weight = Moderate): Indirect biological data compatible with gene disease (reduced enzymatic assay, absent protein on Western Blot or IHC).
P4 / PP4 (Supporting): Clinical phenotype or family history highly specific for the gene-associated disease.
Other criteria (same as V1)
PS1, PS3, PM1, PM2, PM4, PM5, PP2, PP3, BA1, BS1–BS4, BP1–BP5, BP7 — same definitions as ACMG/AMP V1. PP5 and BP6 removed in V2.
Contradictory Criteria (never combine)
PVS1 + PP3 (redundant) | PVS1 + BP1 (mutually exclusive) | PP3 + BP4 (contradictory) | PS3 + BS3 | PM2 + BA1 | PM2 + BS1 | P1 + BS4 | PP2 + BP1 | Multiple modulation levels of same criterion.