SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (Jaganathan et al. 2026)
SpliceAI 1.3.1, position-resolved delta at the effect position, masking off: Five bundled models averaged; GRCh38; masking disabled; donor or acceptor channel chosen by effect type; signed delta (alternative minus reference) at the effect position.
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Evaluations and results
6 evaluations · 16 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) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (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) | 0.65 (best in column) | 0.62 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.73 | Not reported |
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (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) | 0.45 | 0.47 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.36 | Not reported | 0.5 |
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (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 | 0.48 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (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 | 0.66 | Not reported | 0.52 | 0.73 | 0.7 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (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 | 0.71 | 0.68 | 0.74 | Not reported | Not reported | Not reported | Not reported |
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (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 | -0.463 | Not reported | Not reported | Not reported |
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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-spliceai-position-resolved
- areas
- dna-genomes
- contexts
- research
- method types
- supervised_machine_learning
- foundation model eligible
- false
- reported name
- SpliceAI
- version
- 1.3.1, modified by the authors to report position-resolved donor and acceptor predictions for both alleles
- parameters
- Five bundled models averaged; GRCh38; masking disabled; donor or acceptor channel chosen by effect type; signed delta (alternative minus reference) at the effect position. Used for the GTEx and GEL GT/AG, GTEx sQTL and UK Biobank benchmarks.
- source locator
- Methods 'Evaluation of competing methods', SpliceAI paragraph
- provenance note
- SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (Jaganathan et al. 2026), as evaluated in the SpliceAI2 paper.
Related records
- configuration of: SpliceAI
- system: SpliceAI on Genomics England GT/AG cryptic splice activation (auPRC, SpliceAI2 paper)
- system: SpliceAI on GTEx GT/AG (auprc, SpliceAI2 paper)
- system: SpliceAI on GTEx GT/AG (spearman-correlation, SpliceAI2 paper)
- system: SpliceAI on GTEx sQTL (auroc, SpliceAI2 paper)
- system: SpliceAI on GTEx sQTL (spearman-correlation, SpliceAI2 paper)
- system: SpliceAI on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)