Protocol

Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6)

Binary splice-altering classification on the Extended ClinVar benchmark (58,064 variants), scored by sensitivity, specificity, F1 and balanced accuracy.

4 evaluations · 16 results

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4 recorded evaluations, 16 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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All evaluations

4 evaluations · 16 results. Different protocols are not a single leaderboard.

Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) · Dataset: Extended ClinVar benchmark (58,064 variants)

Sorted by Balanced accuracy (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) (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	Balanced accuracy (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset))	F1 (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset))	Recall (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset))	Specificity (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset))
CI-SpliceAI (Fortier et al. 2026)Evaluation	0.895 (best in column)	0.876	0.8	0.991
OpenSpliceAI (Fortier et al. 2026)Evaluation	0.895 (best in column)	0.877 (best in column)	0.799	0.992 (best in column)
SpliceAI (Fortier et al. 2026)Evaluation	0.889	0.865	0.791	0.987
Legacy Ensemble (Fortier et al. 2026)Evaluation	0.809	0.684	0.832 (best in column)	0.787

All 16 result rows with coverage, uncertainty and sources

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Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Original source · PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-fortier2026-protocol-extended-clinvar

areas: dna-genomes
contexts: clinical_research
protocol: Clinical classification as the label after legacy-tool pre-filtering; maximum delta score classification; Legacy Ensemble vote N > 1.
version: Table 6
source locator: Methods 'Extended ClinVar benchmark dataset'; Table 6
limitations: Labels and variant sets are reused from earlier publications. CI-SpliceAI was trained on all human chromosomes, so no benchmark variant is held out from its training; ABCA4 lies on a test chromosome held out by both SpliceAI and OpenSpliceAI (Methods 'Technical overview of deep learning methods'; Discussion).; No uncertainty intervals are printed; significance is from two-proportion Z-tests on accuracy in the Results.

Related records

uses data: Extended ClinVar benchmark (58,064 variants)
assessment: CI-SpliceAI on the Extended ClinVar benchmark (58,064 variants)
assessment: Legacy Ensemble on the Extended ClinVar benchmark (58,064 variants)
assessment: OpenSpliceAI on the Extended ClinVar benchmark (58,064 variants)
assessment: SpliceAI on the Extended ClinVar benchmark (58,064 variants)

Suggest a correction

Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.895 Balanced accuracy (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CI-SpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'CI-SpliceAI', column 'Balanced Accuracy'
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.876 F1 (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CI-SpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'CI-SpliceAI', column 'F1'
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.8 Recall (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CI-SpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'CI-SpliceAI', column 'Sensitivity'
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.991 Specificity (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CI-SpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'CI-SpliceAI', column 'Specificity'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.809 Balanced accuracy (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Legacy Ensemble on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'Legacy Ensemble', column 'Balanced Accuracy'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.684 F1 (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Legacy Ensemble on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'Legacy Ensemble', column 'F1'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.832 Recall (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Legacy Ensemble on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'Legacy Ensemble', column 'Sensitivity'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.787 Specificity (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Legacy Ensemble on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'Legacy Ensemble', column 'Specificity'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.895 Balanced accuracy (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source OpenSpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'OpenSpliceAI', column 'Balanced Accuracy'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.877 F1 (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source OpenSpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'OpenSpliceAI', column 'F1'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.799 Recall (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source OpenSpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'OpenSpliceAI', column 'Sensitivity'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.992 Specificity (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source OpenSpliceAI on the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'OpenSpliceAI', column 'Specificity'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.889 Balanced accuracy (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · 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 the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'SpliceAI', column 'Balanced Accuracy'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.865 F1 (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · 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 the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'SpliceAI', column 'F1'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.791 Recall (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · 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 the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'SpliceAI', column 'Sensitivity'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Extended ClinVar benchmark (58,064 variants) (Fortier et al. Table 6) Dataset: Extended ClinVar benchmark (58,064 variants)	0.987 Specificity (maximum delta score classification after legacy-tool pre-filtering (threshold not restated for this dataset)) fraction · 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 the Extended ClinVar benchmark (58,064 variants) rna-splicing-20261011-fortier2026-protocol-extended-clinvar Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 6, row 'SpliceAI', column 'Specificity'