Evidence Lines¶
Evidence lines in ClinVar-GKS are stored in the evidenceLine bundle section and referenced from statements via hasEvidenceLines arrays of #/evidenceLine/ JSON pointer strings. There are three underlying dict tables that are merged into the single bundle section: gks_dict_evidence_line (SCV), gks_dict_vcv_evidence_line (VCV), and gks_dict_rcv_evidence_line (RCV).
SCV evidence lines appear only on somatic clinical impact (SCI) statements, linking the parent VariantClinicalSignificanceProposition to a specific clinical assertion type — therapeutic response, diagnostic, or prognostic. VCV and RCV evidence lines connect aggregate statements to their contributing and non-contributing evidence items at each aggregation layer.
The ClinvarSomaticEvidenceLine profiles the VA-Spec EvidenceLine with additional properties for the target proposition and evidence outcome.
When Evidence Lines Appear¶
| Statement Category | Has Evidence Lines? |
|---|---|
| Germline classification (PATH, RF, PROT, etc.) | No |
| Oncogenicity (ONCO) | No |
| Somatic clinical impact (SCI) — Tier I or II | Yes |
| Somatic clinical impact (SCI) — Tier III or IV | No (no clinical assertion type) |
Evidence lines are present only on Tier I and Tier II SCI statements, where ClinVar requires at least one clinical assertion type (therapeutic response, diagnostic, or prognostic) to support the tier classification.
Target Propositions¶
Each evidence line carries a proposition specifying the clinical assertion type. These are GA4GH VA-Spec standard types:
| Code | Type | Predicates | Description |
|---|---|---|---|
TR |
VariantTherapeuticResponseProposition | predictsSensitivityTo, predictsResistanceTo |
Response to a specific therapy |
DIAG |
VariantDiagnosticProposition | isDiagnosticInclusionCriterionFor, isDiagnosticExclusionCriterionFor |
Diagnostic relevance |
PROG |
VariantPrognosticProposition | associatedWithBetterOutcomeFor, associatedWithWorseOutcomeFor |
Prognostic significance |
Evidence Outcome¶
The evidenceOutcome field maps the AMP/ASCO/CAP tier to an evidence level:
| Tier | Evidence Outcome |
|---|---|
| Tier I - Strong | Level A/B |
| Tier II - Potential | Level C/D |
Relationship to Parent Statement¶
An SCI statement's structure connects the tiers to the clinical assertions:
SCV Statement
├── proposition: VariantClinicalSignificanceProposition (isClinicallySignificantFor)
├── classification: "Tier I - Strong"
└── hasEvidenceLines:
└── ClinvarSomaticEvidenceLine
├── proposition: VariantTherapeuticResponseProposition (predictsSensitivityTo)
├── evidenceOutcome: "Level A/B"
└── directionOfEvidenceProvided: "supports"
The parent statement asserts clinical significance (the tier), while the evidence line specifies what kind of clinical significance — which therapy, diagnostic criterion, or prognostic outcome the variant is relevant for.
Extensions¶
Somatic evidence lines also carry submittedCondition or submittedConditionSet extensions providing the submitter's original condition details. See SubmittedConditionMapping for the mapping structure.