Protocol

Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of loss-of-function (P classes) versus functional (B classes) variants in the BRCA2 'Both' (coding and noncoding) SNVs stratum, AUROC and AUPRC.

14 evaluations · 28 results

Overview

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

14 recorded evaluations, 28 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

14 evaluations · 28 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) (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; BRCA2 'Both' (coding and noncoding) SNVs)	AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs)
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.739 (best in column)	0.884 (best in column)
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.57	0.838
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.57	0.835
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.558	0.847
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.543	0.817
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.533	0.845
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.4	0.755
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.397	0.76
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.393	0.647
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.369	0.76
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.346	0.752
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.299	0.591
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.228	0.54
NT (Evo 2 paper variant effect evaluations)Evaluation	0.176	0.514

All 28 result rows with coverage, uncertainty and sources

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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: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.739 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CADD on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J561, row 561: Model 'CADD', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.884 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CADD on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I561, row 561: Model 'CADD', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.228 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J573, row 573: Model 'Evo 1', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.54 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I573, row 573: Model 'Evo 1', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.558 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J562, row 562: Model 'Evo 2 40B base', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.847 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I562, row 562: Model 'Evo 2 40B base', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.533 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J563, row 563: Model 'Evo 2 40B', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.845 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I563, row 563: Model 'Evo 2 40B', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.543 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J566, row 566: Model 'Evo 2 7B base', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.817 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I566, row 566: Model 'Evo 2 7B base', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.57 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J565, row 565: Model 'Evo 2 7B', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.835 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I565, row 565: Model 'Evo 2 7B', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.57 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPN-MSA on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J564, row 564: Model 'GPN-MSA', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.838 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPN-MSA on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I564, row 564: Model 'GPN-MSA', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.176 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J574, row 574: Model 'NT', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.514 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I574, row 574: Model 'NT', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.299 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pangolin on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J572, row 572: Model 'Pangolin', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.591 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pangolin on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I572, row 572: Model 'Pangolin', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.397 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J568, row 568: Model 'PhyloP 100', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.76 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I568, row 568: Model 'PhyloP 100', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.346 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J570, row 570: Model 'PhyloP 241', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.752 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I570, row 570: Model 'PhyloP 241', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.369 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J567, row 567: Model 'PhyloP 447', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.76 AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 I567, row 567: Model 'PhyloP 447', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.4 AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) 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 BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-both-snv 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 J569, row 569: Model 'PhyloP 470', Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', 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-brca2-both-snv

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 loss-of-function (P classes) versus functional (B classes) variants in the stratum Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA2', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14); Extended Data Fig. 5c
limitations: Positives: 1156 loss-of-function (P classes); negatives: 5681 functional (B classes); total 6837 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: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)
assessment: CADD on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: NT on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Pangolin on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA2 'Both' (coding and noncoding) SNVs (Evo 2 paper)

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