Protocol

Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of pathogenic/likely pathogenic versus benign/likely benign variants in the ClinVar noncoding indels 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 indels classification (Evo 2 paper, Supplementary Data 1) · Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; ClinVar noncoding indels) (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 indels)	AUROC (zero-shot; ClinVar noncoding indels)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.917 (best in column)	0.971 (best in column)
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.914	0.97
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.849	0.932
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.84	0.934
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.826	0.928
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.82	0.931
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.818	0.928
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.816	0.936
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.711	0.846
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.187	0.513
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.186	0.531
NT (Evo 2 paper variant effect evaluations)Evaluation	0.177	0.505

All 24 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.186 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J86, row 86: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.531 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I86, row 86: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.914 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J78, row 78: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.97 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I78, row 78: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.917 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J77, row 77: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.971 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I77, row 77: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.826 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J83, row 83: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.928 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I83, row 83: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.849 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J81, row 81: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.932 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I81, row 81: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.177 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J88, row 88: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.505 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I88, row 88: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.711 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J85, row 85: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.846 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I85, row 85: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.818 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J84, row 84: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.928 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I84, row 84: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.816 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J79, row 79: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.936 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I79, row 79: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.82 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J82, row 82: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.931 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I82, row 82: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.84 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J80, row 80: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.934 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I80, row 80: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.187 AUPRC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 J87, row 87: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: RNA-FM (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.513 AUROC (zero-shot; ClinVar noncoding indels) 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 indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel 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 I87, row 87: Model 'RNA-FM', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', 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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Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-indel

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 'Indel'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'Indel', Sub_category ''; SI A.3.12 and A.3.13 (page 13); Fig. 3c
limitations: Positives: 682 pathogenic/likely pathogenic; negatives: 3123 benign/likely benign; total 3805 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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