Evaluation

PhyloP 470 on ClinVar noncoding SNVs, far from splice site (Evo 2 paper)

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Evaluation results

1 evaluation · 2 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) · Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site)	AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site)
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.096	0.7

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.096 AUPRC (zero-shot; ClinVar noncoding 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 PhyloP 470 on ClinVar noncoding SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-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 J175, row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.7 AUROC (zero-shot; ClinVar noncoding 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 PhyloP 470 on ClinVar noncoding SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-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 I175, row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site', column 'AUROC'

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)

Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)
Protocol: Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)
Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-14
protocol id: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-far-from-splice-site
dataset version: ClinVar October 2024 release, filtered as in SI A.3.13
split: No split; all variants in the stratum scored
population: ClinVar noncoding SNVs, far from splice site: 336 pathogenic/likely pathogenic, 24449 benign/likely benign, 24785 total
inputs: PhyloP score at the variant; mean over affected reference positions for non-SNVs (SI A.3.12)
adaptation: zero-shot
metric implementation: Not reported
aggregation: Not reported
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No split; all variants in the stratum scored
Adaptation: zero-shot
Scoring implementation: Not reported

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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54 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation zero-shot Context-only references	evo2: Journal full-text XML Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T20:16:14.422554+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `d043dbda49e023ef6b70e36e7ca7832bda6b7af6c5934368e8778a7f23cda8bd` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Comparison: adaptation zero-shot Context-only references	Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx Retrieved: 2026-10-14T12:01:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation zero-shot Context-only references	Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages) Retrieved: 2026-10-14T12:01:04Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `fe2a99108a4ce5c0f4ef1595605eaec709fa86204410d5b66c1384327eb7b925` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Not reported Context-only references	evo2: Journal full-text XML Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T20:16:14.422554+00:00	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `d043dbda49e023ef6b70e36e7ca7832bda6b7af6c5934368e8778a7f23cda8bd` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Comparison: aggregation Not reported Context-only references	Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx Retrieved: 2026-10-14T12:01:04Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Not reported Context-only references	Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages) Retrieved: 2026-10-14T12:01:04Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `fe2a99108a4ce5c0f4ef1595605eaec709fa86204410d5b66c1384327eb7b925` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	evo2: Journal full-text XML Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T20:16:14.422554+00:00	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `d043dbda49e023ef6b70e36e7ca7832bda6b7af6c5934368e8778a7f23cda8bd` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Comparison: budget Not reported Context-only references	Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx Retrieved: 2026-10-14T12:01:04Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `159f321775d634d9ed53b7a81c5cc1b5ef3d407880997e0f8c69bb8315a20a51` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages) Retrieved: 2026-10-14T12:01:04Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `fe2a99108a4ce5c0f4ef1595605eaec709fa86204410d5b66c1384327eb7b925` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version ClinVar October 2024 release, filtered as in SI A.3.13 Context-only references	evo2: Journal full-text XML Original source ↗ Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T20:16:14.422554+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `d043dbda49e023ef6b70e36e7ca7832bda6b7af6c5934368e8778a7f23cda8bd` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

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-eval-phylop-470-clinvar-noncoding-snv-far-from-splice-site

areas: dna-genomes
contexts: research
origin: author_reported
protocol: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-far-from-splice-site
version: Primary source as retrieved 2026-10-14
comparison: protocol id: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-far-from-splice-site; dataset version: ClinVar October 2024 release, filtered as in SI A.3.13; split: No split; all variants in the stratum scored; population: ClinVar noncoding SNVs, far from splice site: 336 pathogenic/likely pathogenic, 24449 benign/likely benign, 24785 total; inputs: PhyloP score at the variant; mean over affected reference positions for non-SNVs (SI A.3.12); adaptation: zero-shot; metric implementation: Not reported; aggregation: Not reported; budget: Not reported
source locator: Supplementary Data 1 (sheet 'Sheet1') row 175: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Far from splice site'
missing metadata: comparison.aggregation: reason: unreported; comparison.budget: reason: unreported; comparison.metric implementation: reason: unreported

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