Baseline: Assess somatic small-variant oncogenicity
Baseline of Assess somatic small-variant oncogenicity
ClinGen/CGC/VICC rules (OncoVI) and SIFT
Baseline method for the use case, reviewed against its cited sources.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field baseline Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field baseline Context-only references | Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2026 final full text in Europe PMC XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids2 values
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids2 values
| Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2026 final full text in Europe PMC XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records3 values
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records3 values
| Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2026 final full text in Europe PMC XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale Somatic oncogenicity is classified with the ClinGen/CGC/VICC points-based standard, which OncoVI applies as fixed rules. For the computational evidence, SIFT scores substitutions from sequence homology with a position-specific scoring matrix and is widely used to prioritise cancer mutations without a trained classifier. Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale Somatic oncogenicity is classified with the ClinGen/CGC/VICC points-based standard, which OncoVI applies as fixed rules. For the computational evidence, SIFT scores substitutions from sequence homology with a position-specific scoring matrix and is widely used to prioritise cancer mutations without a trained classifier. Context-only references | Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2026 final full text in Europe PMC XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Context-only references | Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2026 final full text in Europe PMC XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology · Original source · 2026 final full text in Europe PMC XML
- Comprehensive assessment of computational algorithms in predicting cancer driver mutations · Original source · Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-baseline-somatic-small-variant-oncogenicity
- field
- baseline
- value
- ClinGen/CGC/VICC rules (OncoVI) and SIFT
- source locator
- uc-clinical-20260930-source-oncovi: Methods (IF-ELSE implementation of the points-based SOP); somatic-oncogenicity-20261009-source-chen2020: Table 1 (SIFT position-specific scoring matrix) and Introduction (SIFT widely used in cancer research)
- method ids
- uc-clinical-20260930-method-oncovi; somatic-oncogenicity-20261009-method-sift
- rationale
- Somatic oncogenicity is classified with the ClinGen/CGC/VICC points-based standard, which OncoVI applies as fixed rules. For the computational evidence, SIFT scores substitutions from sequence homology with a position-specific scoring matrix and is widely used to prioritise cancer mutations without a trained classifier.
- review
- method: source-hash-verification; automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that proposed the baseline; no human review claimed; reviewed at: 2026-10-12T18:00:00Z; note: Reviewer corrected rationale. Sources re-retrieved and read; method records and their configuration links checked against the use case's active comparisons. Names the reference newer methods are compared with, not a recommendation. See docs/reviews/use-cases/baselines-2026-10-12.md.
- pins
- record id: somatic-oncogenicity-20261009-source-chen2020; fields: status; attributes.artifact_sha256; sha256: 833a49c39a472927a7666be0840ffbfcc181ac4e986254d673655231f054d331; record id: uc-clinical-20260930-source-oncovi; fields: status; attributes.artifact_sha256; sha256: dad6938e856ad8716c429176c36416ccfc5fb88e76d0e9084c804096a1673d0f; record id: use-case-somatic-small-variant-oncogenicity; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 8ccdc2d3923da8c5aa497bf2a0bd40ccafb89fa8b2f04819228dc52657155359