Configuration

SpliceAI (Alavi 2026)

SPLICEAI as configured in Alavi 2026.

Overview

SpliceAI: SpliceAI annotates sequence variants with predicted splice acceptor and donor changes.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

3 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (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	Accuracy	False positive rate (type I error: false positives as a share of the benign set)	Precision	Proportion (type II error: false negatives as a share of the splicing set (false-negative rate))	Recall	Specificity	Proportion (share of 306 further OPA1 pathogenic substitutions called splice-altering)	Proportion (share of 69 OPA1 VUS substitutions called splice-altering)
SpliceAI (Alavi 2026)Evaluation	Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets), OPA1 LOVD evaluation sets (49 splicing, 79 benign)	95.3% (best in column)	3 (3.8%)	93.9%	3 (6.1%) (best in column)	46 (93.9%) (best in column)	76 (96.2%)	Not reported	Not reported
SpliceAI (Alavi 2026)Evaluation	Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV), Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	94.5%	1 (0.9%) (best in column)	98.5% (best in column)	9 (11.8%)	67 (88.2%)	106 (99.1%) (best in column)	Not reported	Not reported
SpliceAI (Alavi 2026)Evaluation	Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus), OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	75 (24.5%)	6 (8.7%)

All 14 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: SpliceAI (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	94.5% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'SPLICEAI', column 'Accuracy' (PDF page 9 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	98.5% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'SPLICEAI', column 'PPV' (PDF page 9 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	67 (88.2%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'SPLICEAI', column 'Sensitivity' (PDF page 9 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	106 (99.1%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'SPLICEAI', column 'Specificity' (PDF page 9 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	1 (0.9%) False positive rate (type I error: false positives as a share of the benign set) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'SPLICEAI', column 'Type I error' (PDF page 9 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	9 (11.8%) Proportion (type II error: false negatives as a share of the splicing set (false-negative rate)) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'SPLICEAI', column 'Type II error' (PDF page 9 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	95.3% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Accuracy' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	93.9% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'PPV' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	46 (93.9%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Sensitivity' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	76 (96.2%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Specificity' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	3 (3.8%) False positive rate (type I error: false positives as a share of the benign set) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Type I error' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	3 (6.1%) Proportion (type II error: false negatives as a share of the splicing set (false-negative rate)) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Type II error' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus) Dataset: OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	75 (24.5%) Proportion (share of 306 further OPA1 pathogenic substitutions called splice-altering) percent · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) rna-splicing-20261011-alavi2026-protocol-opa1-extended-positive-calls Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Positive mutations' (PDF page 6 of 11)
Configuration: SpliceAI (Alavi 2026)	Protocol: Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus) Dataset: OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	6 (8.7%) Proportion (share of 69 OPA1 VUS substitutions called splice-altering) percent · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) rna-splicing-20261011-alavi2026-protocol-opa1-extended-positive-calls Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'SPLICEAI', column 'Positive VUS' (PDF page 6 of 11)

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Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages)

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-alavi2026-config-spliceai

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: SPLICEAI
foundation model eligible: false
version: Broad Institute SpliceAI-lookup API v1.3.1
parameters: Unmasked delta scores in a 1,000 bp interval (±500 bp); maximum of the four delta scores; threshold > 0.40 by grid search on the OPA1 evaluation sets
access reuse: Public API (SpliceAI-lookup)
source locator: Methods C to H; Table III and IV row label

Related records

configuration of: SpliceAI
system: SpliceAI on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)
system: SpliceAI on OPA1 LOVD evaluation sets (49 splicing, 79 benign)
system: SpliceAI on OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)

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