Configuration
GPN-MSA (Evo 2 paper variant effect evaluations)
Configuration of GPN-MSA: Alignment-based DNA language model; scores SNVs only.
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.
Evaluations and results
26 evaluations · 52 results. Different protocols are not a single leaderboard.
Sorted by AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; BRCA1 coding SNVs) | AUPRC (zero-shot; BRCA1 intronic SNVs) | AUPRC (zero-shot; BRCA1 noncoding SNVs) | AUPRC (zero-shot; BRCA1 splice region SNVs) | AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; BRCA2 coding SNVs) | AUPRC (zero-shot; BRCA2 noncoding SNVs) | AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; ClinVar coding SNVs, far from splice site) | AUPRC (zero-shot; ClinVar coding SNVs, highly conserved) | AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved) | AUPRC (zero-shot; ClinVar coding SNVs, near splice site) | AUPRC (zero-shot; ClinVar coding SNVs, not conserved) | AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved) | AUPRC (zero-shot; ClinVar coding SNVs) | AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs) | AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site) | AUPRC (zero-shot; ClinVar noncoding SNVs, highly conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, intergenic) | AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, near splice site) | AUPRC (zero-shot; ClinVar noncoding SNVs, not conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, poorly conserved) | AUPRC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; SpliceVarDB exonic SNVs) | AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; BRCA1 coding SNVs) | AUROC (zero-shot; BRCA1 intronic SNVs) | AUROC (zero-shot; BRCA1 noncoding SNVs) | AUROC (zero-shot; BRCA1 splice region SNVs) | AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; BRCA2 coding SNVs) | AUROC (zero-shot; BRCA2 noncoding SNVs) | AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; ClinVar coding SNVs, far from splice site) | AUROC (zero-shot; ClinVar coding SNVs, highly conserved) | AUROC (zero-shot; ClinVar coding SNVs, moderately conserved) | AUROC (zero-shot; ClinVar coding SNVs, near splice site) | AUROC (zero-shot; ClinVar coding SNVs, not conserved) | AUROC (zero-shot; ClinVar coding SNVs, poorly conserved) | AUROC (zero-shot; ClinVar coding SNVs) | AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs) | AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site) | AUROC (zero-shot; ClinVar noncoding SNVs, highly conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, intergenic) | AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, near splice site) | AUROC (zero-shot; ClinVar noncoding SNVs, not conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, poorly conserved) | AUROC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; SpliceVarDB exonic SNVs) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | 0.65 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.863 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | 0.579 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.833 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | 0.097 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.653 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | Not reported | 0.775 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.918 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | 0.832 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.891 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | 0.57 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.838 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.446 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.8 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.835 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.905 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.944 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.959 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.932 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.896 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.929 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.896 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.941 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.824 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.748 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.866 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.962 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.896 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.762 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.916 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.708 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.882 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.36 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.915 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.132 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.723 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.994 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.951 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.87 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.884 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.405 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.828 | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.994 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.977 | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.054 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.686 | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.13 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.706 | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), SpliceVarDB experimentally validated splice variants (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.846 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.79 | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1), SpliceVarDB experimentally validated splice variants (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.548 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.675 |
All 52 result rows with coverage, uncertainty and sources
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Evidence
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: configuration of gfm-guides-20261014-gpnmsa-model-gpn-msa Individual claims | Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) Supplementary Data 1 column 'Model' ('GPN-MSA'); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx | source checked ["scope-review"] · 2026-10-14 Audit detailsAccepted with the ten GPN-MSA repoints. See docs/reviews/2026-10-14-gfm-guide-evidence-review.md. Field: Claim: identity-20261014-df16b37d76f1e8d98afd Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Relationship: configuration of gfm-guides-20261014-gpnmsa-model-gpn-msa Individual claims | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Data 1 column 'Model' ('GPN-MSA'); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v2, posted 2024-04-06 | source checked ["scope-review"] · 2026-10-14 Audit detailsAccepted with the ten GPN-MSA repoints. See docs/reviews/2026-10-14-gfm-guide-evidence-review.md. Field: Claim: identity-20261014-df16b37d76f1e8d98afd Source artifact SHA-256: Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Extraction artifact SHA-256: |
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-config-gpn-msa
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- GPN-MSA
- foundation model eligible
- true
- parameters
- Alignment-based DNA language model (reference 92); scores SNVs only
- source locator
- Supplementary Data 1 column 'Model' ('GPN-MSA'); SI A.3.12 (page 13)
- missing metadata
- access reuse: reason: unextracted; checkpoint revision: reason: unreported; version: reason: unreported; note: Checkpoint or release used for variant scoring not stated
- provenance note
- GPN-MSA as scored zero-shot by the Evo 2 authors on human variant effect benchmarks.
Related records
- configuration of: GPN-MSA
- system: GPN-MSA on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA1 coding SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA1 intronic SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA1 noncoding SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA1 splice region SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA2 coding SNVs (Evo 2 paper)
- system: GPN-MSA on BRCA2 noncoding SNVs (Evo 2 paper)
- system: GPN-MSA on ClinVar 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs, far from splice site (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs, highly conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs, moderately conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs, near splice site (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs, not conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar coding SNVs, poorly conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, far from splice site (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, highly conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, intergenic (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, moderately conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, not conserved (Evo 2 paper)
- system: GPN-MSA on ClinVar noncoding SNVs, poorly conserved (Evo 2 paper)
- system: GPN-MSA on SpliceVarDB 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: GPN-MSA on SpliceVarDB exonic SNVs (Evo 2 paper)
- system: GPN-MSA on SpliceVarDB intronic SNVs (Evo 2 paper)
- subject: GPN-MSA (Evo 2 paper): configuration of GPN-MSA