ACMG Assignment¶
Starting with version 13.1.0, Exomiser performs a partial categorisation of the variants contributing to the gene score for a mode of inheritance using the ACMG/AMP Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. The criteria are assigned and combined according to the UK ACGS 2020 guidelines.
It is important to be aware that these scores are not a substitute for manual assignment by a qualified clinical geneticist or clinician - The scores displayed utilise the data found in the Exomiser database and are a subset of the possible criteria by which to assess a variant. Nonetheless, in our benchmarking on the returned cases from the 100K Genomes Project, restricting to variants with these automated P/LP classifications increases precision (positive predictive value) markedly without excluding many real diagnoses. For example, on a cohort of 742 solved cases where the top 5 Exomiser candidates were considered, including the P/LP criteria increased precision 3.8-fold from 15% to 57% with only a small drop in the recall of the diagnoses from 94% to 83%. An even larger 5.7-fold increase of precision from 3% to 17% was observed when considering a larger cohort of 31k cases where only 17% had received a positive diagnosis (again with a modest drop in recall from 91% to 75%).
Exomiser is capable of assigning the following ACMG categories:
Computational and Predictive Data¶
PVS1¶
Variants must have a predicted loss of function effect, be in a gene with known disease associations and have a gene constraint LOF O/E < 0.7635 (gnomAD 2.1.1) to suggest that a gene is LoF intolerant. Variants not predicted to lead to NMD (those located in the last exon) will have the modifier downgraded to Strong.
PM4¶
Stop-loss and in-frame insertions or deletions, not previously assigned a PVS1 criterion are assigned PM4.
PP3 / BP4¶
If REVEL is chosen as a pathogenicity predictor for missense variants, PP3 and BP4 are assigned using the modifiers according to table 2 of Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria. Note that this suggests the use of modifiers up to Strong in the case of pathogenic or Very Strong in the case of benign predictions. Otherwise, an ensemble-based approach will be used for other pathogenicity predictors as per the original 215 guidelines. It should be noted we found better performance using the REVEL-based approach when testing against the 100K genomes data.
Segregation Data¶
BS4¶
If a pedigree with two or more members, including the proband is provided, Exomiser will assign BS4 for variants not segregating with affected members of the family.
De novo Data¶
PS2¶
Exomiser assigns the PS2 criterion for variants compatible with a dominant mode of inheritance, with a pedigree containing at least two ancestors of the proband, none of whom are affected and none of whom share the same allele as the proband.
Population Data¶
BA1¶
Given Exomiser will filter out alleles with an allele frequency of >= 2.0%, this is unlikely to be seen. However, alleles with a maximum frequency >= 5.0% in the frequency sources specified will be assigned the BA1 criterion.
PM2¶
Alleles not present in the ESP, ExAC and 1000 Genomes data sets (i.e. the allele must be absent from all three) are assigned the PM2 criterion.
Allelic Data¶
PM3 / BP2¶
If Exomiser is provided with a phased VCF and a variant is found to be in-trans with a ClinVar Pathogenic variant and associated with a recessive disorder, the PM3 criterion will be applied. However, in cases where variant is being considered for a recessive disorder and is in-cis or a dominant disorder and in-trans with another pathogenic variant the BP2 criterion is applied.
Phenotype¶
PP4¶
Given Exomiser’s focus on phenotype-driven variant prioritisation, variants in a gene associated with a disorder with a phenotype match score > 0.6 to the patient’s phenotype are assigned the PP4 criterion at the Moderate, rather than Supporting level.
Clinical¶
PP5 / BP6¶
If a variant is previously reported as P/LP in ClinVar with a 1-start rating, it will be assigned PP5, those with >= 2 stars (multiple submitters, criteria provided, no conflicts / reviewed by expert panel / practice guideline) will be assigned a Strong level. Conversely, if the variant is previously reported as B/LB it will be assigned BP6 with the same modification criteria. Typically these P/LP variants will be in the Exomiser ClinVar ‘whitelist’, and will have a very high variant score irrespective of the predicted variant effect and always survive any filtering criteria.
Transcript Selection¶
Transcripts will be selected using the most deleterious predicted variant effect from Jannovar according to the transcript-source property set in the application.properties. We recommend using the Ensembl transcript datasource as the Exomiser build uses the GENCODE basic set of transcripts. Future versions should use MANE transcripts.
ACMG assignments will be reported for a variant on a transcript consistent with a particular mode of inheritance in conjunction with a disorder, the assigned criteria with any modifiers and the final classification e.g.
1-12335-A-T, NC_000001.10:g.12335A>T, GENE1(ENST12345678):c.2346A>T:p.1234A>-, PATHOGENIC, [PVS1, PS1, PP4_Strong], Disease (OMIM:12345), AUTOSOMAL_DOMINANT
"acmgAssignments": [
{
"variantEvaluation": {
"genomeAssembly": "HG19",
"contigName": "10",
"start": 123256215,
"end": 123256215,
"ref": "T",
"alt": "G",
"type": "SNV",
"length": 1,
"phredScore": 100,
"variantEffect": "MISSENSE_VARIANT",
"whiteListed": true,
"filterStatus": "PASSED",
"contributesToGeneScore": true,
"variantScore": 1,
"frequencyScore": 1,
"pathogenicityScore": 1,
"predictedPathogenic": true,
"passedFilterTypes": [
"FAILED_VARIANT_FILTER",
"PATHOGENICITY_FILTER",
"FREQUENCY_FILTER",
"VARIANT_EFFECT_FILTER",
"INHERITANCE_FILTER"
],
"frequencyData": {
"rsId": "rs121918506",
"score": 1
},
"pathogenicityData": {
"clinVarData": {
"alleleId": "28333",
"primaryInterpretation": "LIKELY_PATHOGENIC",
"reviewStatus": "criteria provided, single submitter"
},
"score": 0.965,
"predictedPathogenicityScores": [
{
"source": "REVEL",
"score": 0.965
},
{
"source": "MVP",
"score": 0.9517972
}
],
"mostPathogenicScore": {
"source": "REVEL",
"score": 0.965
}
},
"compatibleInheritanceModes": [
"AUTOSOMAL_DOMINANT"
],
"contributingInheritanceModes": [
"AUTOSOMAL_DOMINANT"
],
"transcriptAnnotations": [
{
"variantEffect": "MISSENSE_VARIANT",
"geneSymbol": "FGFR2",
"accession": "ENST00000346997.2",
"hgvsGenomic": "g.12278533A>C",
"hgvsCdna": "c.1688A>C",
"hgvsProtein": "p.(Glu563Ala)",
"rankType": "EXON",
"rank": 12,
"rankTotal": 17
},
{
"variantEffect": "MISSENSE_VARIANT",
"geneSymbol": "FGFR2",
"accession": "ENST00000351936.6",
"hgvsGenomic": "g.12278533A>C",
"hgvsCdna": "c.1688A>C",
"hgvsProtein": "p.(Glu563Ala)",
"rankType": "EXON",
"rank": 13,
"rankTotal": 18
}
]
},
"geneIdentifier": {
"geneId": "ENSG00000066468",
"geneSymbol": "FGFR2",
"hgncId": "HGNC:3689",
"hgncSymbol": "FGFR2",
"entrezId": "2263",
"ensemblId": "ENSG00000066468",
"ucscId": "uc057wle.1"
},
"modeOfInheritance": "AUTOSOMAL_DOMINANT",
"disease": {
"diseaseId": "OMIM:123150",
"diseaseName": "Jackson-Weiss syndrome",
"associatedGeneId": 2263,
"diseaseType": "DISEASE",
"inheritanceMode": "AUTOSOMAL_DOMINANT",
"phenotypeIds": [
"HP:0000006",
"HP:0000272",
"HP:0001363",
"HP:0001783",
"HP:0004691",
"HP:0008080",
"HP:0008122",
"HP:0010055",
"HP:0010743",
"HP:0011800"
],
"id": "OMIM:123150",
"associatedGeneSymbol": "FGFR2"
},
"acmgEvidence": {
"evidence": {
"PM2": "MODERATE",
"PP3": "STRONG",
"PP4": "SUPPORTING",
"PP5": "SUPPORTING"
}
},
"acmgClassification": "LIKELY_PATHOGENIC"
}
]
}