Protocol

Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)

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

Sorted by AUPRC (zero-shot; ClinVar coding microsatellite variants) (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 microsatellite variants)	AUROC (zero-shot; ClinVar coding microsatellite variants)
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.824 (best in column)	0.831
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.82	0.86 (best in column)
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.82	0.856
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.812	0.842
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.773	0.795
ESM-1b (Evo 2 paper variant effect evaluations)Evaluation	0.692	0.814
DeCodon 200M (Evo 2 paper variant effect evaluations)Evaluation	0.582	0.845
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.549	0.762
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.417	0.73
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.359	0.687
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.347	0.696
EnCodon 620M (Evo 2 paper variant effect evaluations)Evaluation	0.275	0.634
ESM-2 650M (Evo 2 paper variant effect evaluations)Evaluation	0.253	0.542
CodonBERT 87M (Evo 2 paper variant effect evaluations)Evaluation	0.244	0.587
NT (Evo 2 paper variant effect evaluations)Evaluation	0.171	0.535

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 microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.244 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J101, row 101: Model 'CodonBERT 87M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: CodonBERT 87M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.587 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I101, row 101: Model 'CodonBERT 87M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: DeCodon 200M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.582 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J91, row 91: Model 'DeCodon 200M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: DeCodon 200M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.845 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I91, row 91: Model 'DeCodon 200M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: EnCodon 620M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.275 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J100, row 100: Model 'EnCodon 620M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: EnCodon 620M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.634 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I100, row 100: Model 'EnCodon 620M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: ESM-1b (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.692 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J94, row 94: Model 'ESM-1b', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: ESM-1b (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.814 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I94, row 94: Model 'ESM-1b', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: ESM-2 650M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.253 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J102, row 102: Model 'ESM-2 650M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: ESM-2 650M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.542 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I102, row 102: Model 'ESM-2 650M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.773 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J95, row 95: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.795 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I95, row 95: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.82 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J89, row 89: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.86 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I89, row 89: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.812 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J92, row 92: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.842 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I92, row 92: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.82 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J90, row 90: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.856 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I90, row 90: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.824 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J93, row 93: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.831 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I93, row 93: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.171 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J103, row 103: Model 'NT', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.535 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I103, row 103: Model 'NT', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.549 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J96, row 96: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.762 AUROC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 I96, row 96: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.359 AUPRC (zero-shot; ClinVar coding microsatellite variants) 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 microsatellite variants (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite 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 J99, row 99: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category '', column 'AUPRC'

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.

Explore all linked results

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: 15

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.

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

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.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-microsatellite

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 'Microsatellite'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'Microsatellite', Sub_category ''; SI A.3.12 and A.3.13 (page 13); Fig. 3b
limitations: Positives: 26 pathogenic/likely pathogenic; negatives: 146 benign/likely benign; total 172 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.

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 microsatellite variants (Evo 2 paper)
assessment: DeCodon 200M on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: EnCodon 620M on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: ESM-1b on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: ESM-2 650M on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: Evo 1 on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: Evo 2 40B base on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: Evo 2 40B on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: Evo 2 7B base on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: Evo 2 7B on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: NT on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: PhyloP 100 on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: PhyloP 241 on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: PhyloP 447 on ClinVar coding microsatellite variants (Evo 2 paper)
assessment: PhyloP 470 on ClinVar coding microsatellite variants (Evo 2 paper)

Suggest a correction