Enigma somatic classification

Applied when the gene and protein change are on the SVIG-UK canonical list (Supplementary Table 3); the class is the list class (Oncogenic or Likely oncogenic).

Stop-gain, frameshift, canonical splice-site and start-loss changes in a gene whose role is tumour suppressor (or both roles) in the IntOGen Compendium of Cancer Genes, or with the UniProt "Tumor suppressor" keyword when IntOGen does not list the gene. Very strong when NMD is expected; Strong in the last exon when more than 10% of the protein is lost, otherwise Moderate; Moderate for a stop in the first 33 codons of exon 1; Strong at a canonical splice site (splice outcome not predicted); Supporting for start loss.

gnomAD v4.1 exomes and genomes. Moderate when the allele is absent; Supporting when its frequency is at most 0.001% in every genetic-ancestry group with more than 100,000 alleles and it is seen at most 1 time in smaller groups. Multi-base substitutions absent from gnomAD are not assessed (gnomAD splits them into single-base parts).

Samples with the allele in public cBioPortal studies (a stand-in for AACR GENIE, which the guideline names). Missense: Strong above 10, Moderate from 5. Truncating and in-frame: Strong above 50, Moderate from 20, Supporting from 10. When O7 comes from GDC residue counts, samples in studies that also feed the GDC are left out. When cBioPortal does not answer and O7 does not apply, GDC cases with the allele are counted instead.

A missense change at a residue where another missense change is on the canonical list. AlphaMissense of this change is compared with the best-scoring canonical change: Moderate when it is equal or higher, within 0.02, or both are at least 0.906; Supporting when it is at least 0.792.

Missense changes with AlphaMissense at least 0.792 (ClinGen-calibrated Supporting), or BayesDel without allele frequency at least 0.13 when AlphaMissense has no score. Not used together with O2. Splice predictions are not used.

Hotspot-like recurrence from NCI GDC open-access mutations (a stand-in for Cancer Hotspots): the residue needs at least 10 cases with a missense change and at least 5 times the cases expected from the gene's missense cases spread evenly along the protein. Strong above 50 cases with at least 10 carrying this change, otherwise Moderate. Without a hotspot, a missense or in-frame change inside a listed critical domain gets Supporting.

Missense changes in genes with gnomAD v4.1 missense Z of at least 3.09; not used when O7 applies.

In-frame insertions and deletions outside UCSC simple repeats and RepeatMasker elements, and stop-loss changes: Moderate.

Needs a reading of published functional studies: chosen by hand.

Needs the tumour's own findings (for POLE exonuclease-domain changes, residues 268–471, a high tumour mutational burden): chosen by hand.

gnomAD v4.1: stand-alone Benign above 1% and Strong above 0.1%, overall or in a continental group (afr, eas, nfe, amr, sas) with more than 2,000 alleles.

Needs knowledge of the gene in this cancer: chosen by hand.

Missense changes with AlphaMissense at most 0.169 (or BayesDel without allele frequency at most -0.18), outside a splice region.

Synonymous changes: Supporting. Strong needs a splice prediction showing no effect, which is not used here, so Strong is chosen by hand.

In-frame insertions and deletions overlapping a UCSC simple repeat or RepeatMasker element: Supporting.

Needs a reading of published functional studies: chosen by hand.

Needs the tumour's own findings: chosen by hand.

Allele counts and numbers in exomes and genomes, by genetic-ancestry group. Used for: O3, B1.

Germline submission counts, somatic clinical impact and oncogenicity classifications for the exact allele. Used for: Tier IV benign consensus, tier evidence.

AlphaMissense and BayesDel (no allele frequency) scores. Used for: O5, O6, B3.

Evidence items and assertions for the variant, its codon, exon and gene. Used for: Tier evidence, evidence table.

Drug-response biomarkers for the allele and the same codon (via MyVariant.info, GRCh37). Used for: Tier evidence, evidence table.

Devices whose biomarker covers the variant exactly, at its codon, a codon range, an exon class or a gene-wide class. Used for: Tier evidence, evidence table.

Samples with the allele and with any missense change at its residue. Used for: O4, evidence section.

Cases with the allele; cases with a missense change at the residue and in the gene. Used for: O7, O4 fallback, evidence section.

Consequence, protein change, exon and protein length on the MANE Select transcript; GRCh37 position. Used for: All codes.

Simple repeats (TRF) and RepeatMasker elements over in-frame indels. Used for: O9, B5.

Gene role (loss of function or activating) across cohorts. Used for: O2.

"Tumor suppressor" and "Proto-oncogene" keywords (genes IntOGen does not list); critical domain coordinates. Used for: O2, O7 domain arm.

Tumour-type hierarchy (codes, names, main types, tissues). Used for: Tumour picker and matching.