Protocol

Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2)

Binary splice-altering classification on the Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3), 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, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) · Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)

Sorted by Balanced accuracy (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) (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 (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound))	F1 (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound))	Recall (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound))	Specificity (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound))	Balanced accuracy (threshold optimised per gene and algorithm for maximum accuracy (upper bound))	F1 (threshold optimised per gene and algorithm for maximum accuracy (upper bound))	Recall (threshold optimised per gene and algorithm for maximum accuracy (upper bound))	Specificity (threshold optimised per gene and algorithm for maximum accuracy (upper bound))
SpliceAI (Fortier et al. 2026)Evaluation	0.836 (best in column)	0.839 (best in column)	0.79 (best in column)	0.883 (best in column)	Not reported	Not reported	Not reported	Not reported
CI-SpliceAI (Fortier et al. 2026)Evaluation	0.794	0.785	0.706	0.883 (best in column)	Not reported	Not reported	Not reported	Not reported
OpenSpliceAI (Fortier et al. 2026)Evaluation	0.746	0.741	0.672	0.819	Not reported	Not reported	Not reported	Not reported
Legacy Ensemble (Fortier et al. 2026)Evaluation	Not reported	Not reported	Not reported	Not reported	0.659	0.609	0.5	0.817

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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-riepe

areas: dna-genomes
contexts: clinical_research
protocol: The delta score matching each variant's effect type is used; thresholds are optimised per gene and algorithm for the highest accuracy (an upper-bound estimate); Legacy Ensemble vote N > 1, and N > 2 for ABCA4.
version: Table 2
source locator: Methods 'Riepe benchmark dataset' and 'Splice prediction tools'; Table 2
limitations: Thresholds optimised on the same data for this benchmark, which may overestimate real-world performance (Discussion 'Study 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.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.794 Balanced accuracy (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'CI-SpliceAI', column 'Balanced Accuracy'
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.785 F1 (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'CI-SpliceAI', column 'F1'
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.706 Recall (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'CI-SpliceAI', column 'Sensitivity'
Configuration: CI-SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.883 Specificity (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'CI-SpliceAI', column 'Specificity'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.659 Balanced accuracy (threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'Legacy Ensemble', column 'Balanced Accuracy'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.609 F1 (threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'Legacy Ensemble', column 'F1'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.5 Recall (threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'Legacy Ensemble', column 'Sensitivity'
Configuration: Legacy Ensemble (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.817 Specificity (threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'Legacy Ensemble', column 'Specificity'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.746 Balanced accuracy (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'OpenSpliceAI', column 'Balanced Accuracy'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.741 F1 (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'OpenSpliceAI', column 'F1'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.672 Recall (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'OpenSpliceAI', column 'Sensitivity'
Configuration: OpenSpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.819 Specificity (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'OpenSpliceAI', column 'Specificity'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.836 Balanced accuracy (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'SpliceAI', column 'Balanced Accuracy'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.839 F1 (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'SpliceAI', column 'F1'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.79 Recall (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'SpliceAI', column 'Sensitivity'
Configuration: SpliceAI (Fortier et al. 2026)	Protocol: Splice-altering variant classification, Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) (Fortier et al. Table 2) Dataset: Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3)	0.883 Specificity (delta score for each variant's effect type; threshold optimised per gene and algorithm for maximum accuracy (upper bound)) 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 Riepe et al. functional splice assay variants (213 variants, ABCA4 and MYBPC3) rna-splicing-20261011-fortier2026-protocol-riepe Aggregation: Not reported Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Table 2, row 'SpliceAI', column 'Specificity'