Configuration

AlphaMissense (Evo 2 paper variant effect evaluations)

Configuration of AlphaMissense: Missense variant effect predictor; scores SNVs at fixed coordinates only.

Overview

An explanatory profile has not yet been reviewed for this record.

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

Evaluations and results

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

Sorted by AUPRC (zero-shot; BRCA1 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	Protocol and dataset	AUPRC (zero-shot; BRCA1 coding SNVs)	AUPRC (zero-shot; BRCA2 coding SNVs)	AUPRC (zero-shot; ClinVar coding SNVs, far from splice site)	AUPRC (zero-shot; ClinVar coding SNVs, highly conserved)	AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved)	AUPRC (zero-shot; ClinVar coding SNVs, near splice site)	AUPRC (zero-shot; ClinVar coding SNVs, not conserved)	AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved)	AUPRC (zero-shot; ClinVar coding SNVs)	AUPRC (zero-shot; SpliceVarDB exonic SNVs)	AUROC (zero-shot; BRCA1 coding SNVs)	AUROC (zero-shot; BRCA2 coding SNVs)	AUROC (zero-shot; ClinVar coding SNVs, far from splice site)	AUROC (zero-shot; ClinVar coding SNVs, highly conserved)	AUROC (zero-shot; ClinVar coding SNVs, moderately conserved)	AUROC (zero-shot; ClinVar coding SNVs, near splice site)	AUROC (zero-shot; ClinVar coding SNVs, not conserved)	AUROC (zero-shot; ClinVar coding SNVs, poorly conserved)	AUROC (zero-shot; ClinVar coding SNVs)	AUROC (zero-shot; SpliceVarDB exonic SNVs)
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.69	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.889	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	Not reported	0.527	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.831	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.977	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.958	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	0.977	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.961	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	Not reported	0.981	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.935	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	Not reported	Not reported	0.914	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.947	Not reported	Not reported	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	0.98	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.931	Not reported	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.9	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.964	Not reported	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.883	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.957	Not reported	Not reported
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1), SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.449	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.594

All 20 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.69 AUPRC (zero-shot; BRCA1 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-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 J607, row 607: Model 'AlphaMissense', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.889 AUROC (zero-shot; BRCA1 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-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 I607, row 607: Model 'AlphaMissense', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
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: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.977 AUPRC (zero-shot; ClinVar 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 ClinVar coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-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 J2, row 2: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.958 AUROC (zero-shot; ClinVar 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 ClinVar coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-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 I2, row 2: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.977 AUPRC (zero-shot; ClinVar coding SNVs, far from splice site) 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 ClinVar coding SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-far-from-splice-site 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 J116, row 116: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.961 AUROC (zero-shot; ClinVar coding SNVs, far from splice site) 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 ClinVar coding SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-far-from-splice-site 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 I116, row 116: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.981 AUPRC (zero-shot; ClinVar coding SNVs, highly conserved) 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 ClinVar coding SNVs, highly conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-highly-conserved 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 J305, row 305: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Highly conserved', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.935 AUROC (zero-shot; ClinVar coding SNVs, highly conserved) 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 ClinVar coding SNVs, highly conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-highly-conserved 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 I305, row 305: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Highly conserved', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.914 AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved) 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 ClinVar coding SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-moderately-conserved 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 J245, row 245: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Moderately conserved', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.947 AUROC (zero-shot; ClinVar coding SNVs, moderately conserved) 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 ClinVar coding SNVs, moderately conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-moderately-conserved 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 I245, row 245: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Moderately conserved', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.98 AUPRC (zero-shot; ClinVar coding SNVs, near splice site) 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 ClinVar coding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-near-splice-site 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 J135, row 135: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.931 AUROC (zero-shot; ClinVar coding SNVs, near splice site) 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 ClinVar coding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-near-splice-site 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 I135, row 135: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.9 AUPRC (zero-shot; ClinVar coding SNVs, not conserved) 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 ClinVar coding SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-not-conserved 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 J365, row 365: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Not conserved', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.964 AUROC (zero-shot; ClinVar coding SNVs, not conserved) 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 ClinVar coding SNVs, not conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-not-conserved 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 I365, row 365: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Not conserved', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.883 AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved) 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 ClinVar coding SNVs, poorly conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-poorly-conserved 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 J425, row 425: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Poorly conserved', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.957 AUROC (zero-shot; ClinVar coding SNVs, poorly conserved) 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 ClinVar coding SNVs, poorly conserved (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-snv-poorly-conserved 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 I425, row 425: Model 'AlphaMissense', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category 'Poorly conserved', column 'AUROC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.449 AUPRC (zero-shot; SpliceVarDB exonic 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-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 J497, row 497: Model 'AlphaMissense', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.594 AUROC (zero-shot; SpliceVarDB exonic 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-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 I497, row 497: Model 'AlphaMissense', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'

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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-config-alphamissense

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: AlphaMissense
foundation model eligible: false
parameters: Missense variant effect predictor (reference 129); scores SNVs at fixed coordinates only
source locator: Supplementary Data 1 column 'Model' ('AlphaMissense'); SI A.3.12 (page 13)
missing metadata: access reuse: reason: unextracted; checkpoint revision: reason: unreported; version: reason: unreported; note: Checkpoint or release used for variant scoring not stated
provenance note: AlphaMissense as scored zero-shot by the Evo 2 authors on human variant effect benchmarks.

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