Protocol

Zero-shot ClinVar noncoding non-SNVs, intergenic 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, intergenic 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, intergenic 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, intergenic) (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, intergenic)	AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic)
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.917 (best in column)	0.875 (best in column)
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.917 (best in column)	0.875 (best in column)
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.893	0.813
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.888	0.875 (best in column)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.875	0.75
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.817	0.75
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.775	0.625
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.732	0.5
NT (Evo 2 paper variant effect evaluations)Evaluation	0.729	0.625
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.71	0.625
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.708	0.625
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.625	0.625

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, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.708 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J229, row 229: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.625 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I229, row 229: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.893 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J224, row 224: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.813 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I224, row 224: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.875 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J225, row 225: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.75 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I225, row 225: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.732 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J232, row 232: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.5 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I232, row 232: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.775 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J228, row 228: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.625 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I228, row 228: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.729 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J230, row 230: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.625 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I230, row 230: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.625 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J227, row 227: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.625 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I227, row 227: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.817 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J226, row 226: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.75 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I226, row 226: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.917 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J222, row 222: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.875 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I222, row 222: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.917 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J223, row 223: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.875 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I223, row 223: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.888 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J221, row 221: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.875 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I221, row 221: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUROC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.71 AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 J231, row 231: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', column 'AUPRC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.625 AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic) 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, intergenic (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-non-snv-intergenic 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 I231, row 231: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'non-SNV', Sub_category 'Intergenic', 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.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 12

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid seeded random ranking; no fitting on assay labels

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Established label-free reference with explicitly permitted sequence/MSA inputs

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

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

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

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Evidence

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Evidence table

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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-intergenic

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 'Intergenic'.
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 'Intergenic'; SI A.3.12 and A.3.13 (page 13); Extended Data Fig. 4
limitations: Positives: 4 pathogenic/likely pathogenic; negatives: 4 benign/likely benign; total 8 variants (Supplementary Data 1).; Label 'Intergenic'; no further definition in the SI.; 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.

Related records

part of: Evo 2 paper zero-shot human variant effect evaluations (Brixi et al. 2026)
uses data: ClinVar October 2024 release, filtered (Brixi et al. 2026)
assessment: Evo 1 on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: Evo 2 40B base on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: Evo 2 40B on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: Evo 2 7B base on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: Evo 2 7B on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: NT on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: Pangolin on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: PhyloP 100 on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: PhyloP 241 on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: PhyloP 447 on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: PhyloP 470 on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)
assessment: RNA-FM on ClinVar noncoding non-SNVs, intergenic (Evo 2 paper)

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