Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1); As published, Nature 652 (2026), Supplementary Data 1

Overview

An explanatory profile has not yet been reviewed for this record.

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

11 recorded evaluations, 22 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

11 evaluations · 22 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) (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	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.6 (best in column)	0.909
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.548	0.915 (best in column)
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.248	0.783
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.234	0.801
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.231	0.779
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.132	0.767
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.129	0.77
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.124	0.779
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.032	0.545
NT (Evo 2 paper variant effect evaluations)Evaluation	0.016	0.51
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.015	0.508

All 22 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.032 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 1 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J661, row 661: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.545 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 1 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I661, row 661: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.548 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B base on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J653, row 653: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.915 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B base on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I653, row 653: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.6 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J654, row 654: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.909 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I654, row 654: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.234 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B base on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J655, row 655: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.801 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B base on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I655, row 655: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.248 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J656, row 656: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.783 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I656, row 656: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.016 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J662, row 662: Model 'NT', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.51 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I662, row 662: Model 'NT', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.132 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 100 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J660, row 660: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.767 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 100 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I660, row 660: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.129 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 241 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J659, row 659: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.77 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 241 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I659, row 659: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.124 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 447 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J658, row 658: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.779 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 447 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I658, row 658: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.231 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 470 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J657, row 657: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.779 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 470 on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I657, row 657: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.015 AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J663, row 663: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUPRC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.508 AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I663, row 663: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category '', column 'AUROC'

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evo2: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages)
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-low-spliceai-pangolin-scores-non-snv

areas: dna-genomes
contexts: research
protocol: Score each variant zero-shot (for Evo 2, the log-likelihood of the variant sequence minus that of the reference over an 8,192-bp genomic window around the variant) and compute AUROC and AUPRC for pathogenic/likely pathogenic versus benign/likely benign variants in the stratum Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Low SpliceAI/Pangolin scores', Variant_Type 'Non-SNV', Sub_category ''; SI A.3.12 and A.3.13 (page 13)
limitations: Positives: 28 pathogenic/likely pathogenic; negatives: 2191 benign/likely benign; total 2219 variants (Supplementary Data 1).; No split: every model scores the same variants zero-shot (SI A.3.12: 'For each benchmark, we score the same variants with all models').; Supervised comparators (AlphaMissense, CADD, SpliceAI, Pangolin) may have been trained on overlapping variants; training overlap is not reported.; No uncertainty is reported.

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