So 2024 VarSome-vs-CanVIG-UK agreement on conflicting BRCA1 missense variants
Each of 450 conflicting BRCA1 missense ClinVar variants independently classified by VarSome and by the CanVIG-UK gene-specific guidance, each consolidated to a three-category scheme (PV/LPV, VUS, BV/LBV); overall concordance measured across the matched pairs.
Overview
Each of 450 conflicting BRCA1 missense ClinVar variants independently classified by VarSome and by the CanVIG-UK gene-specific guidance, each consolidated to a three-category scheme (PV/LPV, VUS, BV/LBV); overall concordance measured across the matched pairs.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
1 recorded evaluation, 2 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 2 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: VarSome vs. CanVIG-UK three-category concordance comparison | Protocol: So 2024 VarSome-vs-CanVIG-UK agreement on conflicting BRCA1 missense variants Dataset: So 2024 BRCA1 conflicting-classification missense cohort | 58.9% concordance_rate percent · higher Uncertainty: type: confidence_interval; level: 95%; low: 52.0; high: 66.4; unit: percent Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSo 2024 VarSome-vs-CanVIG-UK agreement evaluation Not reported Aggregation: Not reported Reinterpretation of Conflicting ClinVar BRCA1 Missense Variants Using VarSome and CanVIG-UK Gene-Specific Guidance · Results, Section 3.3, "Comparison of Classification Results Between Varsome and CanVIG-UK": "The overall concordance rate was 58.9% (95% CI: 52.0-66.4%; 265/450) between VarSome and CanVIG-UK (Figure 2)." |
| Configuration: VarSome vs. CanVIG-UK three-category concordance comparison | Protocol: So 2024 VarSome-vs-CanVIG-UK agreement on conflicting BRCA1 missense variants Dataset: So 2024 BRCA1 conflicting-classification missense cohort | 265 concordant_classification_count count · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSo 2024 VarSome-vs-CanVIG-UK agreement evaluation Not reported Aggregation: Not reported Reinterpretation of Conflicting ClinVar BRCA1 Missense Variants Using VarSome and CanVIG-UK Gene-Specific Guidance · Results, Section 3.3, "Comparison of Classification Results Between Varsome and CanVIG-UK": "The overall concordance rate was 58.9% (95% CI: 52.0-66.4%; 265/450) between VarSome and CanVIG-UK (Figure 2)." |
Source checking is not independent reproduction. Release 2026-10-06-fea06f63ac0e.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
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Recorded evaluations
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Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
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- Author-reported evaluations
- 1
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Null control
Proposed control: requires review
Training-set class prior where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Regularised classifier on simple permitted features, or protocol's conventional reference
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-10-06-fea06f63ac0e. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of uc-clinical-20261005-so-2024-benchmark Individual claims | Reinterpretation of Conflicting ClinVar BRCA1 Missense Variants Using VarSome and CanVIG-UK Gene-Specific Guidance Results, Section 3.3, "Comparison of Classification Results Between Varsome and CanVIG-UK" Version: 2024 published article (Diagnostics (Basel)); CanVIG-UK gene-specific guidance v1.17 / consensus specification v2.17 applied | source checked automated source review · 2026-10-05 Audit detailsTranscription from inspected primary source. No execution, independent replication or human scientific review. Field: Claim: uc-clinical-20261005-so-2024-membership Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
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Release 2026-10-06-fea06f63ac0e · Record review: source checked
1 source records and release history
- Reinterpretation of Conflicting ClinVar BRCA1 Missense Variants Using VarSome and CanVIG-UK Gene-Specific Guidance · Original source · 2024 published article (Diagnostics (Basel)); CanVIG-UK gene-specific guidance v1.17 / consensus specification v2.17 applied
Technical metadata and extraction receipts
Stable ID: uc-clinical-20261005-so-2024-protocol
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- VarSome and CanVIG-UK classifications, each consolidated to three categories, compared pairwise on the same 450-variant conflicting cohort; concordance is the fraction of variants where both tools agree.
- review
- method: automated_source_review; reviewer: Claude Sonnet clinical coverage worker (research-evidence intake); date: 2026-10-05; note: Transcription from inspected primary source. No execution, independent replication or human scientific review.; source id: uc-clinical-20261005-source-so-2024
- limitations
- Measures tool-vs-tool agreement on a conflicting-variant subset, not accuracy against independent ground truth.; A ground-truth-anchored comparator is reported for only 17/450 (3.8%) of variants and is not used in this intake.; No reviewer time or serious-error adjudication reported.