{"entity":{"id":"variant-effect-prediction","kind":"term","name":"Variant effect prediction","aka":["variant effect prediction","variant effect predictor","predicted pathogenicity","in silico pathogenicity prediction","missense effect prediction"],"tldr":"Variant effect prediction uses computation to guess whether a DNA change damages a protein or matters clinically, before or instead of laboratory evidence.","summary":"Variant calling, per Wikipedia, identifies single nucleotide and other variants from sequencing reads; effect prediction is the next step, scoring each variant's likely consequence from conservation, protein structure or, latterly, sequence and protein language models. Predictions feed ACMG-style classification as supporting evidence, and genomic foundation models such as Evo 2 have claimed zero-shot pathogenicity prediction, a claim that has to be tested on held-out variants with clinical labels.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Variant_calling","links":[{"label":"HGVS nomenclature","url":"https://hgvs-nomenclature.org/stable/"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Variant_calling"}],"tags":["cansim-terms"],"related":["clinvar","cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["evo2","nucleotide-transformer"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["variant-calling","hgvs"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/variant-effect-prediction."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Genomics & genetics"},"route":"/terms/variant-effect-prediction/","neighbours":{"collection":[{"id":"clinvar","kind":"collection","name":"ClinVar","route":"/collections/clinvar/"}],"term":[{"id":"autoregressive-modelling","kind":"term","name":"Autoregressive (next-token) modelling","route":"/terms/autoregressive-modelling/"},{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"genomic-and-protein-language-models","kind":"term","name":"Genomic and protein language models: Evo 2, Enformer, ESM","route":"/terms/genomic-and-protein-language-models/"},{"id":"hgvs","kind":"term","name":"HGVS variant nomenclature","route":"/terms/hgvs/"},{"id":"variant-calling","kind":"term","name":"Variant calling","route":"/terms/variant-calling/"},{"id":"zero-shot","kind":"term","name":"Zero-shot prediction","route":"/terms/zero-shot/"}],"technology":[{"id":"evo2","kind":"technology","name":"Evo 2 (Arc Institute, NVIDIA)","route":"/technologies/evo2/"},{"id":"nucleotide-transformer","kind":"technology","name":"Nucleotide Transformer (InstaDeep)","route":"/technologies/nucleotide-transformer/"}]}}