Benchmark
Evo 2 paper zero-shot human variant effect evaluations (Brixi et al. 2026)
Zero-shot classification of human variants from ClinVar, SpliceVarDB and BRCA1/BRCA2 functional assays, scored with Evo 2 and comparison models by the Evo 2 authors; AUROC and AUPRC per variant stratum in Supplementary Data 1.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results on linked records
This benchmark has no results of its own in this release. 37 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 16 evaluations · 32 results
- Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 14 evaluations · 28 results
- Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 10 evaluations · 20 results
- Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 10 evaluations · 20 results
- Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 15 evaluations · 30 results
- Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 18 evaluations · 36 results
- Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 11 evaluations · 22 results
- Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 13 evaluations · 26 results
- Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 12 evaluations · 24 results
- Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Protocol · part of this benchmark · 14 evaluations · 28 results
9 further linked records are listed under Related records.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 98 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding non-SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
- Zero-shot SpliceVarDB intronic SNVs classification (Evo 2 paper, Supplementary Data 1) · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- evo2: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
- Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages)
- Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-evo2-brixi2026-benchmark-human-vep
- areas
- dna-genomes
- contexts
- research
- entity level
- suite
- version
- As published, Nature 652 (2026)
- task
- Classify pathogenic or loss-of-function human variants from benign or functional variants by zero-shot model scores
- scope note
- Protocols are the variant strata of Supplementary Data 1; one evaluation per model and stratum.
- source locator
- Main text 'Human variant effect prediction' and Fig. 3 legend; Supplementary Information A.3.12 to A.3.15; Supplementary Data 1
Related records
- part of: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding non-SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)
- part of: Zero-shot SpliceVarDB intronic SNVs classification (Evo 2 paper, Supplementary Data 1)