.. _acmg_assignment: =============== 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 Variant Classification Guidance `_ `updated 2020 guidelines `_. Additionally, splice variants are scored according to `Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup `_. In this case Exomiser will assign the PVS1, PS1, PP3, BP4, BP7 categories. 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: Variant Classification Evidence =============================== These categories are taken from Figure 1. of `Richards et al. 2015 `_, those in **bold** are assigned by Exomiser. Population Data =============== For the population data criteria, all frequencies are considered using the populations set by the user in the :ref:`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 --- `MAF is too high for disorder` 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. BS1 --- `MAF is too high for disorder` Assigned to autosomal variants with a maximum non-founder population allele frequency >= 1.5% or mitochondrial variants with MAF >= 5% BS2 --- `Observation in controls inconsistent with disease penetrance` Variants with a MAF < 5% (not BA1) which have a gnomAD non-founder population `hom` count > 5 when considered under an autosomal dominant model (gene score) or > 2 when considered under autosomal recessive, X-recessive or X-dominant are assigned a `BS2`. PM2 --- `Absent in population databases` In accordance with the `updated PM2 guidance `_, variants absent from all of the user-defined :ref:`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`. PS4 --- `Prevalence in affecteds statistically increased over controls` Not assigned Computational and Predictive Data ================================= PVS1 ---- `Predicted null variant in a gene where LOF is a known mechanism of disease` 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 --- `Same amino acid change as an established pathogenic variant` 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. Splice variants will be assigned PS1 with Strong, Moderate or Supporting modifiers, according to table 2 of `Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup `_. PM4 --- `Protein length changing variant` Stop-loss and in-frame insertions or deletions, not previously assigned a `PVS1` criterion are assigned `PM4`. PM5 --- `Novel missense change at an amino acid residue where a different pathogenic missense change has been seen before` 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 --------- `Multiple lines of computational evidence support a deleterious effect on the gene/gene product (PP3)` `Multiple lines of computational evidence suggest no impact on gene product (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. For splice variants outside of the +/-1,2 canonical splice donor/acceptor site are assigned `PP3` with a SpliceAI score >= 0.2 or `BP4` with a SpliceAI score < 0.1 BP1 --- `Missense in gene where only truncating cause disease` Missense or inframe indels found in a gene in which >=75% of ClinVar P/LP variants are loss of function variants are assigned `BP1`. BP7 --- `Silent variant with non predicted splice impact` For synonymous variants, `BP7` is assigned if the variant is not reported as P/LP in ClinVar, with a 1+ star rating and has a SpliceAI score < 0.1 For splice region variants Exomiser follows the recommendations made in `Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup `_ In this case, non-donor/acceptor splice region variants with a SpliceAI score < 0.1 which have been assigned BP4 at or beyond the +7 and −21 positions (conservative designation for donor/acceptor splice region) are also assigned a `BP7`. Functional Data =============== PS3 --- `Well-established functional studies show a deleterious effect` Not assigned PM1 --- `Mutational hot spot or well-studied functional domain without benign variation` 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`. PP2 --- `Missense in gene with low rate of benign missense variants and path. missenses common` Missense or inframe indels in genes where >= 75% of ClinVar P/LP variants are missense and ClinVar benign missense variants make up <=5% of all reported missense ClinVar variants (P/LP/VUS/B/LB) in that gene are assigned a `PP2` BS3 --- `Well-established functional studies show no deleterious effect` Not assigned Segregation Data ================ PP1 --- `Co-segregation with disease in multiple affected family members` Not assigned BS4 --- `Non-segregation with disease` Not assigned. Previously this was assigned but the pedigree assignment of 'affected' status was not always reliable so this is no longer applied automatically. De novo Data ============ PS2 --- `*De novo* (paternity & maternity confirmed)` 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. PM6 --- `*De novo* (without paternity & maternity confirmed)` Not assigned Allelic Data ============ PM3 / BP2 --------- `Observed in *trans* with a dominant variant` `Observed in *cis* with a pathogenic variant` For recessive disorders, detected in *trans* with a pathogenic variant *PM3* 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 --- `Patient's phenotype or FH highly specific for gene` 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. BP5 --- `Found in case with an alternate cause` Not assigned Clinical ======== PP5 / BP6 --------- `Reputable source w/out shared data = benign (BP6)` `Reputable source = pathogenic (PP5)` 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 transcripts for hg19/GRCh37 and MANE transcripts for hg38/GRCh38. 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. .. parsed-literal:: 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 .. code-block:: json "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" } ] }