Protocol

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

Zero-shot classification of pathogenic/likely pathogenic versus benign/likely benign variants in the ClinVar 'Both' (coding and noncoding) indels stratum, AUROC and AUPRC.

10 evaluations · 20 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

10 recorded evaluations, 20 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

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All evaluations

10 evaluations · 20 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar 'Both' (coding and 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 'Both' (coding and 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 'Both' (coding and noncoding) indels)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) indels)
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.995 (best in column)	0.983 (best in column)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.995	0.983
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.993	0.968
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.992	0.961
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.968	0.839
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.968	0.836
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.966	0.835
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.966	0.837
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.918	0.655
NT (Evo 2 paper variant effect evaluations)Evaluation	0.852	0.505

All 20 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 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.918 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J595, row 595: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.655 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I595, row 595: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.995 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J587, row 587: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.983 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I587, row 587: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.995 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J588, row 588: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.983 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I588, row 588: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.992 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J590, row 590: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.961 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I590, row 590: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.993 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J589, row 589: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.968 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I589, row 589: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.852 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J596, row 596: Model 'NT', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and 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 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I596, row 596: Model 'NT', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.968 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J593, row 593: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.836 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I593, row 593: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.966 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J592, row 592: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.837 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I592, row 592: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.966 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J594, row 594: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.835 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I594, row 594: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.968 AUPRC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 J591, row 591: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUPRC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.839 AUROC (zero-shot; ClinVar 'Both' (coding and 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 'Both' (coding and noncoding) indels (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 I591, row 591: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category '', column 'AUROC'

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Author-reported evaluations: 10

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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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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-both-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 'Both', Variant_Type 'Indel'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Both', Variant_Type 'Indel', Sub_category ''; SI A.3.12 and A.3.13 (page 13)
limitations: Positives: 21955 pathogenic/likely pathogenic; negatives: 3546 benign/likely benign; total 25501 variants (Supplementary Data 1).; The 'Both' rows are larger than the sum of the coding and noncoding rows; the population is not explained in the source.; No split: every model scores the same variants zero-shot (SI A.3.12: 'For each benchmark, we score the same variants with all models').; Supervised comparators (AlphaMissense, CADD, SpliceAI, Pangolin) may have been trained on overlapping variants; training overlap is not reported.; No uncertainty is reported.

Related records

part of: Evo 2 paper zero-shot human variant effect evaluations (Brixi et al. 2026)
uses data: ClinVar October 2024 release, filtered (Brixi et al. 2026)
assessment: Evo 1 on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: Evo 2 40B base on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: Evo 2 40B on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: Evo 2 7B base on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: Evo 2 7B on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: NT on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: PhyloP 100 on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: PhyloP 241 on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: PhyloP 447 on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)
assessment: PhyloP 470 on ClinVar 'Both' (coding and noncoding) indels (Evo 2 paper)

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