Protocol

Zero-shot BRCA2 coding 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 coding SNVs stratum, AUROC and AUPRC.

15 evaluations · 30 results

Overview

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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.

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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 BRCA2 coding 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 coding 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 coding SNVs)	AUROC (zero-shot; BRCA2 coding SNVs)
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	0.527 (best in column)	0.831 (best in column)
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.446	0.8
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.402	0.787
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.346	0.77
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.333	0.768
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.325	0.752
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.306	0.727
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.296	0.736
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.281	0.741
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.259	0.694
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.256	0.726
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.208	0.56
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.179	0.545
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.157	0.535
NT (Evo 2 paper variant effect evaluations)Evaluation	0.134	0.501

All 30 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: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.527 AUPRC (zero-shot; BRCA2 coding 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 AlphaMissense on BRCA2 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J531, row 531: Model 'AlphaMissense', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.831 AUROC (zero-shot; BRCA2 coding 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 AlphaMissense on BRCA2 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I531, row 531: Model 'AlphaMissense', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.402 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J533, row 533: Model 'CADD', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.787 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I533, row 533: Model 'CADD', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.157 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J544, row 544: Model 'Evo 1', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.535 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I544, row 544: Model 'Evo 1', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding 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 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J534, row 534: Model 'Evo 2 40B base', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.77 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I534, row 534: Model 'Evo 2 40B base', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.333 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J535, row 535: Model 'Evo 2 40B', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.768 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I535, row 535: Model 'Evo 2 40B', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.259 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J541, row 541: Model 'Evo 2 7B base', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.694 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I541, row 541: Model 'Evo 2 7B base', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.306 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J539, row 539: Model 'Evo 2 7B', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.727 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I539, row 539: Model 'Evo 2 7B', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.446 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J532, row 532: Model 'GPN-MSA', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.8 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I532, row 532: Model 'GPN-MSA', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.134 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J545, row 545: Model 'NT', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.501 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I545, row 545: Model 'NT', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.179 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J543, row 543: Model 'Pangolin', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.545 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I543, row 543: Model 'Pangolin', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.325 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J536, row 536: Model 'PhyloP 100', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding 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 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I536, row 536: Model 'PhyloP 100', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.256 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J540, row 540: Model 'PhyloP 241', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.726 AUROC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 I540, row 540: Model 'PhyloP 241', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.281 AUPRC (zero-shot; BRCA2 coding 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 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 J537, row 537: Model 'PhyloP 447', Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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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

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Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-brca2-coding-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 'Coding', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA2', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14)
limitations: Positives: 611 loss-of-function (P classes); negatives: 3879 functional (B classes); total 4490 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: AlphaMissense on BRCA2 coding SNVs (Evo 2 paper)
assessment: CADD on BRCA2 coding SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA2 coding SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA2 coding SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA2 coding SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA2 coding SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA2 coding SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA2 coding SNVs (Evo 2 paper)
assessment: NT on BRCA2 coding SNVs (Evo 2 paper)
assessment: Pangolin on BRCA2 coding SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA2 coding SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA2 coding SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA2 coding SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA2 coding SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA2 coding SNVs (Evo 2 paper)

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