Configuration
SpliceAI (Evo 2 paper variant effect evaluations)
Configuration of SpliceAI: Supervised splicing predictor.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
14 evaluations · 28 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 noncoding SNVs, highly conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved) | 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 noncoding SNVs, highly conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved) | 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) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SpliceAI (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) | 0.508 | Not reported | 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 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.284 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.55 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.357 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.876 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.862 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.965 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.901 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.947 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.393 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.647 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.208 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.56 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.89 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.939 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.998 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.987 | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.913 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.967 | Not reported | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.75 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.973 | Not reported | Not reported | Not reported |
| SpliceAI (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 | 0.856 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.966 | Not reported | Not reported |
| SpliceAI (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 | 0.974 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.961 | Not reported |
| SpliceAI (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 | 0.919 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.934 |
All 28 result rows with coverage, uncertainty and sources
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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-config-spliceai
- areas
- dna-genomes
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- SpliceAI
- foundation model eligible
- false
- parameters
- Supervised splicing predictor (reference 130)
- source locator
- Supplementary Data 1 column 'Model' ('SpliceAI'); 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
- SpliceAI as scored zero-shot by the Evo 2 authors on human variant effect benchmarks.
Related records
- configuration of: SpliceAI
- system: SpliceAI on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: SpliceAI on BRCA1 coding SNVs (Evo 2 paper)
- system: SpliceAI on BRCA1 intronic SNVs (Evo 2 paper)
- system: SpliceAI on BRCA1 noncoding SNVs (Evo 2 paper)
- system: SpliceAI on BRCA1 splice region SNVs (Evo 2 paper)
- system: SpliceAI on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: SpliceAI on BRCA2 coding SNVs (Evo 2 paper)
- system: SpliceAI on BRCA2 noncoding SNVs (Evo 2 paper)
- system: SpliceAI on ClinVar noncoding SNVs (Evo 2 paper)
- system: SpliceAI on ClinVar noncoding SNVs, highly conserved (Evo 2 paper)
- system: SpliceAI on ClinVar noncoding SNVs, moderately conserved (Evo 2 paper)
- system: SpliceAI on ClinVar noncoding SNVs, not conserved (Evo 2 paper)
- system: SpliceAI on ClinVar noncoding SNVs, poorly conserved (Evo 2 paper)
- system: SpliceAI on SpliceVarDB 'Both' (coding and noncoding) SNVs (Evo 2 paper)
- system: SpliceAI on SpliceVarDB exonic SNVs (Evo 2 paper)
- system: SpliceAI on SpliceVarDB intronic SNVs (Evo 2 paper)