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 according to the UK ACGS 2020 guidelines and scored according to the ClinGen SVI updated 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 4.0) 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.
PS1
Variants with the same amino acid change as previously reported P/LP missense or in-frame indel ClinVar variants will be assigned PS1 with a strength of Strong for variants >= 2 stars, Moderate for variants with 1 star or Supporting for those without a ClinVar start rating.
PM4
Stop-loss and in-frame insertions or deletions, not previously assigned a PVS1 criterion are assigned PM4.
PM5
Variants having a novel missense change to an amino acid where a previously reported ClinVar P/LP variant has been seen will be assigned PM5 with a strength of Moderate for those with >=2 stars or Supporting otherwise.
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.
Functional Data
PM1
Missense and inframe indels are assigned PM1 if the surrounding region of 25 nucleotides either side of the variant contain at least 4 reported P/LP variants in ClinVar and no B/LB variants. If the number of P/LP variants is greater than the number of VUS in the region the strength will be assigned Moderate but regions containing P/LP <= VUS (and no B/BL) will have the strength downgraded to Supporting.
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
For the population data criteria, all frequencies are considered using the populations set by the user in the frequencySources:, apart from any bottle-necked populations not recommended for frequency filtering from gnomAD according to their filtering allele frequency document. This excludes the Ashkenazi Jewish (ASJ), European Finnish (FIN), Other (OTH), Amish (AMI) and Middle Eastern (MID) populations. In addition the LOCAL frequency will also not be used.
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. Variants listed as being excluded from this category by the ClinGen SVI working group BA1 exclusion list will not be marked as BA1, assuming they survived variant filtering.
PM2
In accordance with the updated PM2 guidance, variants absent from all of the user-defined frequencySources: will be assigned the PM2_Supporting criterion. Additionally, for variants considered under a recessive mode of inheritance they can have a frequency of < 0.01% (0.0001) in all non-bottlenecked populations to be assigned PM2_Supporting.
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",
"frequencyScore": 1
},
"pathogenicityData": {
"clinVarData": {
"alleleId": "28333",
"primaryInterpretation": "LIKELY_PATHOGENIC",
"reviewStatus": "criteria provided, single submitter"
},
"pathogenicitycore": 0.965,
"pathogenicityScores": [
{
"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"
}
]
}