Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026)
Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx · Peer-reviewed
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Results
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Claims
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- GPN-MSA (Evo 2 paper): configuration of GPN-MSA: Configuration of GPN-MSA (Supplementary Data 1 column 'Model' ('GPN-MSA'); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract))
Models, benchmarks and other records
Configurations (21)
- AlphaMissense (Evo 2 paper variant effect evaluations)
- CADD (Evo 2 paper variant effect evaluations)
- CodonBERT 87M (Evo 2 paper variant effect evaluations)
- DeCodon 200M (Evo 2 paper variant effect evaluations)
- EnCodon 620M (Evo 2 paper variant effect evaluations)
- ESM-1b (Evo 2 paper variant effect evaluations)
- ESM-2 650M (Evo 2 paper variant effect evaluations)
- Evo 1 (Evo 2 paper variant effect evaluations)
- Evo 2 7B (Evo 2 paper variant effect evaluations)
- Evo 2 7B base (Evo 2 paper variant effect evaluations)
- Evo 2 40B (Evo 2 paper variant effect evaluations)
- Evo 2 40B base (Evo 2 paper variant effect evaluations)
- GPN-MSA (Evo 2 paper variant effect evaluations)
- NT (Evo 2 paper variant effect evaluations)
- Pangolin (Evo 2 paper variant effect evaluations)
- PhyloP 100 (Evo 2 paper variant effect evaluations)
- PhyloP 241 (Evo 2 paper variant effect evaluations)
- PhyloP 447 (Evo 2 paper variant effect evaluations)
- PhyloP 470 (Evo 2 paper variant effect evaluations)
- RNA-FM (Evo 2 paper variant effect evaluations)
- SpliceAI (Evo 2 paper variant effect evaluations)
Benchmarks (1)
Protocols (49)
- Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding non-SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)
- Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)
Datasets (4)
Evaluations (705)
- AlphaMissense on BRCA1 coding SNVs (Evo 2 paper)
- AlphaMissense on BRCA2 coding SNVs (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs, far from splice site (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs, highly conserved (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs, moderately conserved (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs, near splice site (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs, not conserved (Evo 2 paper)
- AlphaMissense on ClinVar coding SNVs, poorly conserved (Evo 2 paper)
- AlphaMissense on SpliceVarDB exonic SNVs (Evo 2 paper)
- CADD on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- CADD on BRCA1 coding SNVs (Evo 2 paper)
- CADD on BRCA1 intronic SNVs (Evo 2 paper)
- CADD on BRCA1 noncoding SNVs (Evo 2 paper)
- CADD on BRCA1 splice region SNVs (Evo 2 paper)
- CADD on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- CADD on BRCA2 coding SNVs (Evo 2 paper)
- CADD on BRCA2 noncoding SNVs (Evo 2 paper)
- CADD on ClinVar 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- CADD on ClinVar coding SNVs (Evo 2 paper)
- CADD on ClinVar coding SNVs, far from splice site (Evo 2 paper)
- CADD on ClinVar coding SNVs, highly conserved (Evo 2 paper)
- CADD on ClinVar coding SNVs, moderately conserved (Evo 2 paper)
- CADD on ClinVar coding SNVs, near splice site (Evo 2 paper)
- CADD on ClinVar coding SNVs, not conserved (Evo 2 paper)
Evidence
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Evidence table
Inspect claims, sources and review details
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27 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51 Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-026-10176-5/MediaObjects/41586_2026_10176_MOESM3_ESM.xlsx Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1038/s41586-026-10176-5 Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-NC-ND-4.0 Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations9 values
| Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-14T12:01:04Z Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.review.artifact_sha256 159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51 Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Review: date 2026-10-14 Source metadata | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) No field-specific location recorded Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the issue #129 Evo 2 evidence pass.
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-evo2-brixi2026-source-supplementary-data-1
- areas
- dna-genomes
- contexts
- research
- url
- https://doi.org/10.1038/s41586-026-10176-5
- artifact url
- https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-026-10176-5/MediaObjects/41586_2026_10176_MOESM3_ESM.xlsx
- version
- Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx
- retrieved at
- 2026-10-14T12:01:04Z
- artifact sha256
- 159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51
- doi
- 10.1038/s41586-026-10176-5
- publication status
- peer_reviewed
- licence
- CC-BY-NC-ND-4.0
- media type
- application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
- source locator
- Sheet 'Sheet1', A1:J706
- limitations
- Variant counts in Supplementary Data 1 differ from the counts in the Fig. 3 legend: ClinVar coding SNVs 14,313 (legend 14,319), noncoding SNVs 33,747 (legend 34,761), coding non-SNVs 978 (legend 1,236), noncoding non-SNVs 3,623 (legend 3,894); SpliceVarDB exonic 1,179 (legend 1,181) and intronic 3,708 (legend 3,769); BRCA1 coding SNVs 2,768 (legend 2,077). BRCA1 noncoding (1,125) and BRCA1 all SNVs (3,893) match the legend and Supplementary Information A.3.15.; The ClinVar rows with Genomic_Feature 'Both' (SNV 89,126; Indel 25,501; Microsatellite 618 variants) are larger than the sum of the coding and noncoding rows (SNV 48,060), so 'Both' is not the union of the coding and noncoding strata; the source does not explain the difference.; Coding Indel (1,150) plus coding Microsatellite (172) rows do not sum to the coding non-SNV row (978); the relation between the 'non-SNV', 'Indel' and 'Microsatellite' strata is not stated.; Sub_category labels 'Poorly conserved' and 'Not conserved' do not match the bin names in Supplementary Information A.3.13 ('weakly conserved', 0 <= phyloP < 0.5; 'accelerated evolution', phyloP < 0); the mapping is not stated.; Model label spelling differs within the sheet: 'phyloP 100/241/447/470' on SpliceVarDB rows and 'PhyloP 100/241/447/470' elsewhere.; AUROC and AUPRC cells store full-precision doubles and carry the number format '0.000', so the workbook displays three decimals.; No uncertainty (confidence interval or standard error) is given for any value.; Licence CC BY-NC-ND 4.0 (article licence statement); no archived copy kept in the batch folder.; Independent review 2026-10-14: the results of four strata (ClinVar noncoding SNVs, ClinVar coding non-SNVs, ClinVar noncoding non-SNVs, SpliceVarDB intronic SNVs) are disputed. Their variant counts differ from the Fig. 3 legend and the Supplementary Table 6 and 7 values for Evo 2 7B base differ from the workbook. ClinVar coding SNVs (14,313 against 14,319), SpliceVarDB exonic (1,179 against 1,181) and BRCA1 coding SNVs (2,768 against 2,077) also differ from the legend, but their Supplementary Table 6 to 8 values agree with the workbook and, for BRCA1, 2,768 plus 1,125 noncoding equals the n = 3,893 of Fig. 3f; they are not disputed.
- review
- method: source-hash-verification; method note: Re-downloaded from the publisher on 2026-10-14; SHA-256 matches.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-14; artifact sha256: 159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51; retrieval url: https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-026-10176-5/MediaObjects/41586_2026_10176_MOESM3_ESM.xlsx; note: Independent review 2026-10-14.