Dataset

OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)

OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) as assembled by Alavi 2026.

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12 evaluations · 24 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 OPA1 LOVD substitutions outside the evaluation sets: 306 pathogenic or likely pathogenic mutations and 69 variants of uncertain significance, without splicing labels Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Results D 'Positional Variant classification across the OPA1 corpus'; Table III header 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 Results D 'Positional Variant classification across the OPA1 corpus'; Table III header Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Results D 'Positional Variant classification across the OPA1 corpus'; Table III header 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 ↗ Results D 'Positional Variant classification across the OPA1 corpus'; Table III header 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 ↗ Results D 'Positional Variant classification across the OPA1 corpus'; Table III header 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 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) as assembled by Alavi 2026. Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Results D 'Positional Variant classification across the OPA1 corpus'; Table III header 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 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ Results D 'Positional Variant classification across the OPA1 corpus'; Table III header 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-extended-corpus

areas: dna-genomes
contexts: clinical_research
version: As assembled by Alavi 2026
population: OPA1 LOVD substitutions outside the evaluation sets: 306 pathogenic or likely pathogenic mutations and 69 variants of uncertain significance, without splicing labels
split: No split
source locator: Results D 'Positional Variant classification across the OPA1 corpus'; Table III header

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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: 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)	66 (21.6%) 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Positive mutations' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (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)	7 (10.1%) 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 AlphaGenome (Either Module) 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 'ALPHAGENOME (EITHER MODULE)', column 'Positive VUS' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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)	54 (17.6%) 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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Positive mutations' (PDF page 6 of 11)
Configuration: AlphaGenome Junction Scorer (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)	4 (5.8%) 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 AlphaGenome Junction Scorer 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 'ALPHAGENOME JUNCTION SCORER', column 'Positive VUS' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	58 (19.0%) 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Positive mutations' (PDF page 6 of 11)
Configuration: AlphaGenome Splice Scorer (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)	5 (7.2%) 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 AlphaGenome Splice Scorer 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 'ALPHAGENOME SPLICE SCORER', column 'Positive VUS' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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)	70 (22.9%) 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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Positive mutations' (PDF page 6 of 11)
Configuration: Borzoi (128-bp) (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)	13 (18.8%) 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 Borzoi (128-bp) 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 'BORZOI (128-BP)', column 'Positive VUS' (PDF page 6 of 11)
Configuration: Borzoi (32-bp) (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)	86 (28.1%) 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 Borzoi (32-bp) 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 'BORZOI (32-BP)', column 'Positive mutations' (PDF page 6 of 11)
Configuration: Borzoi (32-bp) (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)	7 (10.1%) 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 Borzoi (32-bp) 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 'BORZOI (32-BP)', column 'Positive VUS' (PDF page 6 of 11)
Configuration: Evo2 40B (human identifier) (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)	276 (90.2%) 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 Evo2 40B (human identifier) 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 'EVO2 40B (HU. IDENT.)', column 'Positive mutations' (PDF page 6 of 11)
Configuration: Evo2 40B (human identifier) (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)	47 (68.1%) 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 Evo2 40B (human identifier) 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 'EVO2 40B (HU. IDENT.)', column 'Positive VUS' (PDF page 6 of 11)
Configuration: Evo2 40B (without human identifier) (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)	280 (91.5%) 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 Evo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Positive mutations' (PDF page 6 of 11)
Configuration: Evo2 40B (without human identifier) (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)	46 (66.7%) 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 Evo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Positive VUS' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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)	104 (34.0%) 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Positive mutations' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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)	25 (36.2%) 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Positive VUS' (PDF page 6 of 11)
Configuration: Genos 10B (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)	92 (30.1%) 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 Genos 10B 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 'GENOS 10B', column 'Positive mutations' (PDF page 6 of 11)
Configuration: Genos 10B (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)	23 (33.3%) 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 Genos 10B 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 'GENOS 10B', column 'Positive VUS' (PDF page 6 of 11)
Configuration: NTv3 650M Post (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)	77 (25.2%) 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 NTv3 650M Post 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 'NTV3 650M POST', column 'Positive mutations' (PDF page 6 of 11)
Configuration: NTv3 650M Post (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)	9 (13.0%) 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 NTv3 650M Post 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 'NTV3 650M POST', column 'Positive VUS' (PDF page 6 of 11)
Configuration: NTv3 650M Pre (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)	212 (69.3%) 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 NTv3 650M Pre 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 'NTV3 650M PRE', column 'Positive mutations' (PDF page 6 of 11)
Configuration: NTv3 650M Pre (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)	23 (33.3%) 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 NTv3 650M Pre 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 'NTV3 650M PRE', column 'Positive VUS' (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)