Configuration

Genos 10B ClinVar (Alavi 2026)

GENOS 10B CLINVAR as configured in Alavi 2026.

Overview

Genos: Human-centric mixture-of-experts genomic model trained on human de novo assemblies with a 1 Mb context, which models sequence at single-nucleotide resolution and predicts effects of noncoding variants on RNA expression.

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

Evaluations and results

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

Sorted by Accuracy (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Accuracy	False positive rate (type I error: false positives as a share of the benign set)	Precision	Proportion (type II error: false negatives as a share of the splicing set (false-negative rate))	Recall	Specificity	Proportion (share of 306 further OPA1 pathogenic substitutions called splice-altering)	Proportion (share of 69 OPA1 VUS substitutions called splice-altering)
Genos 10B ClinVar (Alavi 2026)Evaluation	Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets), OPA1 LOVD evaluation sets (49 splicing, 79 benign)	66.4% (best in column)	9 (11.4%) (best in column)	62.5% (best in column)	34 (69.4%)	15 (30.6%)	70 (88.6%) (best in column)	Not reported	Not reported
Genos 10B ClinVar (Alavi 2026)Evaluation	Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV), Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	56.3%	31 (28.7%)	46.6%	49 (64.5%) (best in column)	27 (35.5%) (best in column)	76 (71.0%)	Not reported	Not reported
Genos 10B ClinVar (Alavi 2026)Evaluation	Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus), OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	104 (34.0%)	25 (36.2%)

All 14 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Genos 10B ClinVar (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	56.3% 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 Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'GENOS 10B CLINVAR', column 'Accuracy' (PDF page 9 of 11)
Configuration: Genos 10B ClinVar (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	46.6% 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 Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'GENOS 10B CLINVAR', column 'PPV' (PDF page 9 of 11)
Configuration: Genos 10B ClinVar (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	27 (35.5%) 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 Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'GENOS 10B CLINVAR', column 'Sensitivity' (PDF page 9 of 11)
Configuration: Genos 10B ClinVar (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	76 (71.0%) 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 Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'GENOS 10B CLINVAR', column 'Specificity' (PDF page 9 of 11)
Configuration: Genos 10B ClinVar (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	31 (28.7%) 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 Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'GENOS 10B CLINVAR', column 'Type I error' (PDF page 9 of 11)
Configuration: Genos 10B ClinVar (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	49 (64.5%) 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 Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'GENOS 10B CLINVAR', column 'Type II error' (PDF page 9 of 11)
Configuration: Genos 10B ClinVar (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)	66.4% 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Accuracy' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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)	62.5% 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'PPV' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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%) 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Sensitivity' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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)	70 (88.6%) 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Specificity' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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)	9 (11.4%) 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Type I error' (PDF page 6 of 11)
Configuration: Genos 10B ClinVar (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%) 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 Genos 10B ClinVar 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 'GENOS 10B CLINVAR', column 'Type II error' (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)

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

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-alavi2026-config-genos-10b-clinvar

areas: dna-genomes
contexts: clinical_research
method types: foundation_model
reported name: GENOS 10B CLINVAR
foundation model eligible: true
version: Zhejiang Lab ClinVar-based probability API (version not printed)
parameters: ClinVar-trained pathogenicity probability from the Zhejiang Lab API (DCS Cloud); threshold >= 0.63
access reuse: Zhejiang Lab API through the DCS Cloud catalog
source locator: Methods C to H; Table III and IV row label
fine tuning: applied: true; note: ClinVar-based pathogenicity probability from the Zhejiang Lab API; training details not printed (Methods H)

Related records

configuration of: Genos
system: Genos 10B ClinVar on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)
system: Genos 10B ClinVar on OPA1 LOVD evaluation sets (49 splicing, 79 benign)
system: Genos 10B ClinVar on OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)

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