Carrier plasma protein levels for rare splice-region variants, UK Biobank (SpliceAI2 paper, Pearson)
Pearson correlation between model score (loss positive, gain negative) at the nearest canonical splice site and mean carrier protein z-score for 6,149 rare splice-region variants; more negative means a closer match to reduced protein.
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.
4 recorded evaluations, 4 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
4 evaluations · 4 results. Different protocols are not a single leaderboard.
Protocol: Carrier plasma protein levels for rare splice-region variants, UK Biobank (SpliceAI2 paper, Pearson) · Dataset: UK Biobank rare splice-region variants with carrier plasma protein levels (Jaganathan et al. 2026)
Sorted by Pearson (with mean carrier plasma protein z-score; more negative is better) (lower 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 | Pearson (with mean carrier plasma protein z-score; more negative is better) |
|---|---|
| SpliceAI2 two-model multispecies ensemble (Jaganathan et al. 2026)Evaluation | -0.504 (best in column) |
| AlphaGenome raw composite splice score, maximum aggregation (Jaganathan et al. 2026)Evaluation | -0.481 |
| Pangolin, per-position score at the effect position, masking off (Jaganathan et al. 2026)Evaluation | -0.475 |
| SpliceAI 1.3.1, position-resolved delta at the effect position, masking off (Jaganathan et al. 2026)Evaluation | -0.463 |
All 4 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 4
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set class prior where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Regularised classifier on simple permitted features, or protocol's conventional reference
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
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-protocol-ukb-proteomics
- areas
- dna-genomes
- contexts
- research
- protocol
- VEP splice-region variants with allele frequency <= 0.1% carried by at least two individuals with Olink measurements; per-gene residualised protein levels; carriers of other rare coding variants in the gene excluded; Pearson between score and mean carrier z-score.
- version
- bioRxiv v1 Fig. 3f
- metric
- pearson-correlation
- metric direction
- lower
- source locator
- Methods 'UK Biobank proteomics analysis'; Fig. 3f
- limitations
- Proxy endpoint: plasma protein abundance, not a measured splicing outcome.; Developer-reported: the SpliceAI2 authors (Illumina) built the benchmark, chose comparator settings and ran every model; AlphaGenome was scored by co-authors at the University of Oxford.; Training overlap: SpliceAI2 was trained on all human genes except those on chromosomes 21 and 22, and the benchmark is genome-wide, so most variants lie in genes seen in training.; Essential splice variants are excluded, so results do not cover canonical GT/AG disruption.; No confidence intervals or resampling uncertainty are printed.; Preprint (bioRxiv v1), not peer reviewed.
Related records
- uses data: UK Biobank rare splice-region variants with carrier plasma protein levels (Jaganathan et al. 2026)
- assessment: AlphaGenome on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)
- assessment: Pangolin on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)
- assessment: SpliceAI on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)
- assessment: SpliceAI2 on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)