Class | Pathogenicity | Criteria |
---|---|---|
5 | Clearly pathogenic | 1. Reported in the literature as pathogenic with supporting evidence; multiple independent cases, pedigree segregation studies and/or functional analysis AND |
2. Phenotype and inheritance pattern in patient correlates with the gene | ||
4 | Likely to be pathogenic | 1. Not described in the literature, or weak evidence for pathogenicity in published literature; no segregation or functional analysis available AND |
2. Phenotype and inheritance pattern in patient correlates with the gene AND | ||
3. Location of variant in gene and pathogenic mechanism are compatible with previously described pathogenic variants in the gene AND | ||
4. Minor allele frequency (MAF) is <1Â % in dbSNP (v142) and <1Â % in Exome Variant Server (EVS, v6500) AND | ||
5. a) Missense variant; conserved amino acid, Polyphen 2 (HumVar) and SIFT concur in predicting deleterious effect or three or more of five splice prediction toolsa return >10Â % difference in splice site prediction value between wild type and variant OR | ||
b) Frameshift or nonsense variant; where expected mechanism is loss of function OR | ||
c) Synonymous or intronic change; nucleotide highly conserved across multiple species and three or more splice prediction tools return >10Â % difference in splice site prediction value between wild type and variant | ||
3 | Unknown significance (VoUS) | 1. Minor allele frequency <1Â % in dbSNP (v142) and EVS (v6500) AND |
2. Phenotype and inheritance pattern in patient correlates with the gene AND | ||
3. Not described in the literature, or described in literature with inconclusive or no evidence AND | ||
a) In silico predictions score variants as Class 4 but phenotype does not correlate with the gene OR | ||
b) In silico predictions are conflicting (for example; conserved amino acid, very low MAF but Polyphen 2 and SIFT predict benign) | ||
2 | Unlikely to be pathogenic | 1. a) Minor allele frequency is between 1Â % and 3Â % in dbSNP (v142) and/or between 1Â % and 3Â % in EVS (v6500) but phenotype and/or inheritance pattern in patient correlates with the gene OR |
 b) Minor allele frequency is <1 % in dbSNP and EVS but phenotype and/or inheritance pattern in patient does not correlate with gene AND | ||
2. a) Missense variant; amino acid is weakly conserved across multiple species and/or Polyphen 2 (HumVar) and SIFT concur in predicting benign OR | ||
 b) Synonymous or intronic change; nucleotide weakly conserved across multiple species and splice prediction toolsa show no significant difference between wild type and variant, even if MAF is <1 % on dbSNP and EVS AND | ||
3. a) Some evidence for benign status in literature but weak or inconclusive AND/OR b) Some evidence that variant does not segregate with disease in pedigree of patient(s) tested in this cohort | ||
1 | Clearly not pathogenic | Frequency >3Â % in dbSNP (v142) or >3Â % in Exome Variant Server (v6500) OR |
Frequency <3Â % but described and proven as not pathogenic in published literature |