Stop-gain variants for which the 50 bp rule predicts nonsense-mediated decay: 32,362 pathogenic and 198 benign in the Fig. 6d legend (32,441 pathogenic in the Methods).
3 evaluations · 3 results. Different protocols are not a single leaderboard.
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Source dataset label ClinVar stop-gains Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Source dataset label ClinVar stop-gains Context-only references | Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz |
| Source dataset label ClinVar stop-gains Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Source location Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Source location Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Context-only references | Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz |
| Source location Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Split Whole labelled set; no training on labels Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Split Whole labelled set; no training on labels Context-only references | Brandes et al. 2023 Supplementary Information (Supplementary Table 1 and Methods) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-information.pdf.gz |
| Split Whole labelled set; no training on labels Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Subset scope Stop-gain variants for which the 50 bp rule predicts nonsense-mediated decay: 32,362 pathogenic and 198 benign in the Fig. 6d legend (32,441 pathogenic in the Methods). Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 'Contents', column AUC_NMD; Fig. 6d legend; Methods 'AUC metrics for pathogenicity classification', paragraph on bootstrapping the stop-gain ROC-AUC Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: gfm-guides-20261014-esm1b-data-clinvar-stop-gains-nmd