# Variant effect prediction

Source: https://onco.cc/terms/variant-effect-prediction/  
OnCo record `variant-effect-prediction` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

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.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: variant effect prediction; variant effect predictor; predicted pathogenicity; in silico pathogenicity prediction; missense effect prediction
- Tags: cansim-terms

## 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.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Variant_calling
- HGVS nomenclature: https://hgvs-nomenclature.org/stable/
- Wikipedia: https://en.wikipedia.org/wiki/Variant_calling

## Connected records

- collections: [ClinVar](https://onco.cc/collections/clinvar/)
- terms: [Autoregressive (next-token) modelling](https://onco.cc/terms/autoregressive-modelling/), [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Genomic and protein language models: Evo 2, Enformer, ESM](https://onco.cc/terms/genomic-and-protein-language-models/), [HGVS variant nomenclature](https://onco.cc/terms/hgvs/), [Variant calling](https://onco.cc/terms/variant-calling/), [Zero-shot prediction](https://onco.cc/terms/zero-shot/)
- technologies: [Evo 2 (Arc Institute, NVIDIA)](https://onco.cc/technologies/evo2/), [Nucleotide Transformer (InstaDeep)](https://onco.cc/technologies/nucleotide-transformer/)

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JSON: https://onco.cc/api/v1/entities/variant-effect-prediction.json