Protocol

Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of pathogenic/likely pathogenic versus benign/likely benign variants in the ClinVar noncoding non-SNVs, moderately conserved stratum, AUROC and AUPRC.

12 evaluations · 24 results

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.

12 recorded evaluations, 24 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

12 evaluations · 24 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) · Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) (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 noncoding non-SNVs, moderately conserved)	AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved)
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.872 (best in column)	0.96 (best in column)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.862	0.958
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.784	0.884
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.723	0.888
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.475	0.725
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.335	0.776
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.329	0.783
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.318	0.776
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.28	0.7
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.182	0.528
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.165	0.508
NT (Evo 2 paper variant effect evaluations)Evaluation	0.164	0.502

All 24 result rows with coverage, uncertainty and sources

Filter evaluations

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 noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.165 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J303, row 303: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.508 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I303, row 303: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.872 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J293, row 293: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.96 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I293, row 293: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.862 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J294, row 294: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.958 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I294, row 294: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.723 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J295, row 295: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.888 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I295, row 295: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.784 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J296, row 296: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.884 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I296, row 296: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.164 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J304, row 304: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.502 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I304, row 304: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.475 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pangolin on ClinVar noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J300, row 300: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.725 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pangolin on ClinVar noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I300, row 300: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.28 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J301, row 301: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.7 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I301, row 301: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.329 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J297, row 297: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.783 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I297, row 297: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.318 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J298, row 298: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.776 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I298, row 298: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.335 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J299, row 299: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.776 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I299, row 299: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.182 AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 J302, row 302: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.528 AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved) 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 noncoding non-SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-moderately-conserved 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 I302, row 302: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved', column 'AUROC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

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Author-reported evaluations: 12

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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

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

3 source records and release history

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-noncoding-non-snv-moderately-conserved

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 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Moderately conserved'; SI A.3.12 and A.3.13 (page 13); Extended Data Fig. 4
limitations: Positives: 109 pathogenic/likely pathogenic; negatives: 625 benign/likely benign; total 734 variants (Supplementary Data 1).; 0.5 <= phyloP 100-way <= 2 (SI A.3.13).; 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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