Protocol

Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of pathogenic/likely pathogenic versus benign/likely benign variants in the ClinVar coding non-SNVs, not conserved stratum, AUROC and AUPRC.

15 evaluations · 30 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.

15 recorded evaluations, 30 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

15 evaluations · 30 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) · Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved)	AUROC (zero-shot; ClinVar coding non-SNVs, not conserved)
DeCodon 200M (Evo 2 paper variant effect evaluations)Evaluation	0.959 (best in column)	0.927 (best in column)
EnCodon 620M (Evo 2 paper variant effect evaluations)Evaluation	0.894	0.796
CodonBERT 87M (Evo 2 paper variant effect evaluations)Evaluation	0.856	0.734
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.835	0.767
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.835	0.757
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.832	0.77
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.825	0.771
ESM-2 650M (Evo 2 paper variant effect evaluations)Evaluation	0.758	0.633
ESM-1b (Evo 2 paper variant effect evaluations)Evaluation	0.713	0.512
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.61	0.529
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.583	0.517
NT (Evo 2 paper variant effect evaluations)Evaluation	0.577	0.52
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.57	0.632
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.564	0.529
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.519	0.667

All 30 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: CodonBERT 87M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.856 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 CodonBERT 87M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J404, row 404: Model 'CodonBERT 87M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: CodonBERT 87M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.734 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 CodonBERT 87M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I404, row 404: Model 'CodonBERT 87M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: DeCodon 200M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.959 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 DeCodon 200M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J398, row 398: Model 'DeCodon 200M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: DeCodon 200M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.927 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 DeCodon 200M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I398, row 398: Model 'DeCodon 200M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: EnCodon 620M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.894 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 EnCodon 620M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J399, row 399: Model 'EnCodon 620M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: EnCodon 620M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.796 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 EnCodon 620M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I399, row 399: Model 'EnCodon 620M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: ESM-1b (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.713 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 ESM-1b on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J412, row 412: Model 'ESM-1b', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: ESM-1b (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.512 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 ESM-1b on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I412, row 412: Model 'ESM-1b', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: ESM-2 650M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.758 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 ESM-2 650M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J406, row 406: Model 'ESM-2 650M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: ESM-2 650M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.633 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 ESM-2 650M on ClinVar coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I406, row 406: Model 'ESM-2 650M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.564 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J409, row 409: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.529 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I409, row 409: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.835 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J402, row 402: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.767 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I402, row 402: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.835 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J403, row 403: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.757 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I403, row 403: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.832 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J401, row 401: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.77 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I401, row 401: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.825 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J400, row 400: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.771 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I400, row 400: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.577 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J410, row 410: Model 'NT', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.52 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I410, row 410: Model 'NT', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.519 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J405, row 405: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.667 AUROC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 I405, row 405: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.583 AUPRC (zero-shot; ClinVar coding non-SNVs, not 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 coding non-SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-not-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 J411, row 411: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved', column 'AUPRC'

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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-coding-non-snv-not-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 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Not conserved'; SI A.3.12 and A.3.13 (page 13); Extended Data Fig. 4
limitations: Positives: 73 pathogenic/likely pathogenic; negatives: 49 benign/likely benign; total 122 variants (Supplementary Data 1).; Label 'Not conserved'; SI A.3.13 names its bins 'weakly conserved' (0 <= phyloP < 0.5) and 'accelerated evolution' (phyloP < 0); the mapping is not stated.; 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: CodonBERT 87M on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: DeCodon 200M on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: EnCodon 620M on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: ESM-1b on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: ESM-2 650M on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: Evo 1 on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: Evo 2 40B base on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: Evo 2 40B on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: Evo 2 7B base on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: Evo 2 7B on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: NT on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: PhyloP 100 on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: PhyloP 241 on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: PhyloP 447 on ClinVar coding non-SNVs, not conserved (Evo 2 paper)
assessment: PhyloP 470 on ClinVar coding non-SNVs, not conserved (Evo 2 paper)

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