Configuration
AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)
AlphaGenome raw composite splice score, maximum aggregation: 1 Mb sequence context centred on the variant; SPLICE_SITES, SPLICE_SITE_USAGE and SPLICE_JUNCTIONS scorers via score_variant() and predict_variant(); composite = splice site + splice site usage + one fifth of splice junction effect.
Overview
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Evaluations and results
7 evaluations · 17 results. Different protocols are not a single leaderboard.
Sorted by Spearman (all variants; essential splice variants excluded) (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 | Spearman (all variants; essential splice variants excluded) | Spearman (exonic variants; essential splice variants excluded) | AUPRC (all variants; essential splice variants excluded) | AUPRC (all variants) | AUPRC (deep intronic variants (500 bp or more from the nearest exon); essential splice variants excluded) | AUPRC (exonic variants; essential splice variants excluded) | AUPRC (near intronic variants (under 500 bp from the nearest exon); essential splice variants excluded) | AUROC (all variants; essential splice variants excluded) | AUROC (exonic variants; essential splice variants excluded) | AUROC (intronic variants; essential splice variants excluded) | Pearson (with mean carrier plasma protein z-score; more negative is better) | Spearman (deep intronic variants (500 bp or more from the nearest exon); essential splice variants excluded) | Spearman (intronic variants; essential splice variants excluded) | Spearman (near intronic variants (under 500 bp from the nearest exon); essential splice variants excluded) | Spearman (with multi-cohort raw allele count in high-pLI genes; more negative is better) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | GTEx v8 fine-mapped sQTL effect size prediction (SpliceAI2 paper, Spearman), GTEx v8 sQTL fine-mapped and null SNVs near junction ends (Jaganathan et al. 2026) | 0.68 (best in column) | 0.64 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.76 | Not reported | Not reported |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | Cryptic splice site usage among RNA-seq-confirmed GT/AG-creating SNVs, GTEx (SpliceAI2 paper, Spearman), GTEx rare GT/AG-creating SNVs with RNA-seq cryptic splicing labels (Jaganathan et al. 2026) | 0.41 | 0.43 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.31 | Not reported | 0.47 | Not reported |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | Cryptic splice site activation by rare GT/AG-creating variants in Genomics England blood RNA-seq (SpliceAI2 paper, auPRC), Genomics England rare-disease participants with WGS and blood RNA-seq (Jaganathan et al. 2026) | 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 |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | Cryptic splice site activation by rare GT/AG-creating SNVs, GTEx WGS and RNA-seq (SpliceAI2 paper, auPRC), GTEx rare GT/AG-creating SNVs with RNA-seq cryptic splicing labels (Jaganathan et al. 2026) | Not reported | Not reported | 0.54 | Not reported | 0.45 | 0.56 | 0.58 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | GTEx v8 fine-mapped sQTL SNVs against non-prioritised SNVs near junction ends (SpliceAI2 paper, auROC), GTEx v8 sQTL fine-mapped and null SNVs near junction ends (Jaganathan et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.73 | 0.71 | 0.76 | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | Depletion of high-scoring splice-proximal SNVs in gnomAD, TOPMed and UK Biobank, high-pLI genes (SpliceAI2 paper, Spearman), gnomAD, TOPMed and UK Biobank splice-proximal SNV depletion set (Jaganathan 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 | -0.105 |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | Carrier plasma protein levels for rare splice-region variants, UK Biobank (SpliceAI2 paper, Pearson), UK Biobank rare splice-region variants with carrier plasma protein levels (Jaganathan et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | -0.481 | Not reported | Not reported | Not reported | Not reported |
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How it works, versions and access
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
1 source record and release history
- A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Technical metadata and extraction receipts
Stable ID: rna-splicing-20261013-spliceai2-config-alphagenome-composite-max
- areas
- dna-genomes
- contexts
- research
- method types
- supervised_machine_learning
- foundation model eligible
- false
- reported name
- AlphaGenome
- parameters
- 1 Mb sequence context centred on the variant; SPLICE_SITES, SPLICE_SITE_USAGE and SPLICE_JUNCTIONS scorers via score_variant() and predict_variant(); composite = splice site + splice site usage + one fifth of splice junction effect; raw outputs, maximum aggregation; chosen from 40 scoring configurations as best on average across eight evaluations
- access reuse
- Run at the University of Oxford by co-authors (Y.K., E.M.W.; supervised by S.J.S.)
- source locator
- Methods 'Evaluation of competing methods', AlphaGenome paragraph; Author contributions
- missing metadata
- version: reason: unreported; note: API or weights version not printed.
- provenance note
- AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026), as evaluated in the SpliceAI2 paper.
Related records
- configuration of: AlphaGenome
- subject: AlphaGenome scoring in the SpliceAI2 paper
- system: AlphaGenome on Genomics England GT/AG cryptic splice activation (auPRC, SpliceAI2 paper)
- system: AlphaGenome on GTEx GT/AG (auprc, SpliceAI2 paper)
- system: AlphaGenome on GTEx GT/AG (spearman-correlation, SpliceAI2 paper)
- system: AlphaGenome on GTEx sQTL (auroc, SpliceAI2 paper)
- system: AlphaGenome on GTEx sQTL (spearman-correlation, SpliceAI2 paper)
- system: AlphaGenome on splice-proximal SNV depletion in high-pLI genes (Spearman, SpliceAI2 paper)
- system: AlphaGenome on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)