Protocol

Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of loss-of-function (LOF) versus functional or intermediate (FUNC, INT) variants in the BRCA1 intronic 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 BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; BRCA1 intronic 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; BRCA1 intronic SNVs)	AUROC (zero-shot; BRCA1 intronic SNVs)
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.438 (best in column)	0.895 (best in column)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.424	0.888
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.362	0.813
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.357	0.876
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.348	0.834
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.32	0.885
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.194	0.869
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.097	0.653
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.084	0.637
NT (Evo 2 paper variant effect evaluations)Evaluation	0.072	0.688
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.065	0.711
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.058	0.748
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.057	0.677
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.024	0.465
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.016	0.389

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: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.362 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J700, row 700: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.813 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I700, row 700: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.024 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J696, row 696: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.465 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I696, row 696: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.438 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J694, row 694: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.895 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I694, row 694: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.424 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J695, row 695: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.888 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I695, row 695: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.194 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J692, row 692: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.869 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I692, row 692: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.32 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J693, row 693: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.885 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I693, row 693: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.097 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J698, row 698: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.653 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I698, row 698: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.072 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J697, row 697: Model 'NT', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.688 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I697, row 697: Model 'NT', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.348 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J706, row 706: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.834 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I706, row 706: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.084 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J701, row 701: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.637 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I701, row 701: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.057 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J702, row 702: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.677 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I702, row 702: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.058 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J703, row 703: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.748 AUROC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 I703, row 703: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.065 AUPRC (zero-shot; BRCA1 intronic 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 BRCA1 intronic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 J704, row 704: Model 'PhyloP 470', Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Author-reported evaluations: 15

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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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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-brca1-intronic-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 (LOF) versus functional or intermediate (FUNC, INT) variants in the stratum Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA1', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14); Extended Data Fig. 5b
limitations: Positives: 9 loss-of-function (LOF); negatives: 480 functional or intermediate (FUNC, INT); total 489 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: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)
assessment: CADD on BRCA1 intronic SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA1 intronic SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA1 intronic SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA1 intronic SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA1 intronic SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA1 intronic SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA1 intronic SNVs (Evo 2 paper)
assessment: NT on BRCA1 intronic SNVs (Evo 2 paper)
assessment: Pangolin on BRCA1 intronic SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA1 intronic SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA1 intronic SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA1 intronic SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA1 intronic SNVs (Evo 2 paper)
assessment: RNA-FM on BRCA1 intronic SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA1 intronic SNVs (Evo 2 paper)

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