Dataset

OPA1 LOVD evaluation sets (49 splicing, 79 benign)

OPA1 LOVD evaluation sets (49 splicing, 79 benign) as assembled by Alavi 2026.

Evaluation results

12 evaluations · 72 results. Different protocols are not a single leaderboard.

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Population 49 OPA1 single-nucleotide substitutions annotated 'consequence: splicing defect' and 79 benign or likely benign substitutions from LOVD (retrieved 2026-04-15), GRCh38, NM_015560.2 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Methods A 'Dataset selection and curation'; Table I Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Source location Methods A 'Dataset selection and curation'; Table I Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Methods A 'Dataset selection and curation'; Table I Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Split No split Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Methods A 'Dataset selection and curation'; Table I Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Version As assembled by Alavi 2026 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Methods A 'Dataset selection and curation'; Table I Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Description OPA1 LOVD evaluation sets (49 splicing, 79 benign) as assembled by Alavi 2026. Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Methods A 'Dataset selection and curation'; Table I Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Name OPA1 LOVD evaluation sets (49 splicing, 79 benign) Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Methods A 'Dataset selection and curation'; Table I Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

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-data-opa1-evaluation-sets

areas: dna-genomes
contexts: clinical_research
version: As assembled by Alavi 2026
population: 49 OPA1 single-nucleotide substitutions annotated 'consequence: splicing defect' and 79 benign or likely benign substitutions from LOVD (retrieved 2026-04-15), GRCh38, NM_015560.2
split: No split
source locator: Methods A 'Dataset selection and curation'; Table I

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaGenome (Either Module) (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)	88.3% 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Accuracy' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (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)	90.5% 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'PPV' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (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)	38 (77.6%) 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Sensitivity' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (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)	75 (94.9%) 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Specificity' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (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)	4 (5.1%) 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Type I error' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (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)	11 (22.4%) 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Type II error' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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)	85.2% 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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Accuracy' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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)	91.7% 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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'PPV' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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)	33 (67.3%) 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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Sensitivity' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Specificity' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Type I error' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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)	16 (32.7%) 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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Type II error' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	86.7% 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Accuracy' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	94.4% 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'PPV' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	34 (69.4%) 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Sensitivity' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	77 (97.5%) 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Specificity' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	2 (2.5%) 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Type I error' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	15 (30.6%) 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Type II error' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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)	89.1% 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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Accuracy' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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)	92.9% 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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'PPV' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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)	39 (79.6%) 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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Sensitivity' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Specificity' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Type I error' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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)	10 (20.4%) 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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Type II error' (PDF page 6 of 11)
Configuration: Borzoi (32-bp) (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)	91.4% 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 Borzoi (32-bp) 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 'BORZOI (32-BP)', column 'Accuracy' (PDF page 6 of 11)