Examples¶
Annotated example files are maintained in the examples/ directory of the repository. These serve as reference targets for the data structures produced by the pipeline and are useful for early adopters and for validating output against expected formats.
Categorical Variants (Cat-VRS)¶
Examples of CategoricalVariant records — the resolved VRS representations of ClinVar variations with expressions, cross-references, and metadata.
| File | Variant | Type | Description |
|---|---|---|---|
| clinvar:12582.jsonc | KRAS (variation 12582) | CanonicalAllele | Canonical allele with DefiningAlleleConstraint, multiple expression formats, gene associations, cross-references |
| clinvar:208366.jsonc | Variation 208366 | CanonicalAllele | Additional canonical allele example |
See Categorical Variants output reference for field documentation.
SCV Statements¶
Examples of VA-Spec Statement records for individual ClinVar submissions.
Germline Pathogenicity (G.01)¶
| File | SCV | Classification | Gene / Condition | Description |
|---|---|---|---|---|
| SCV001571657.2 (path).jsonc | SCV001571657.2 | Pathogenic (definitive) | KRAS / Acute myeloid leukemia | VariantPathogenicityProposition, NOCP review status, gene context with HGNC mapping, MedGen/Orphanet/MeSH/MONDO condition xrefs |
Germline Other Types (G.02-G.09)¶
| File | SCV | Classification | Type | Description |
|---|---|---|---|---|
| SCV004035006.2 (assoc).jsonc | SCV004035006.2 | association (supports) | Association (G.06) | ClinVarAssociationProposition, KRAS variant with multiple endometrial conditions in a ConditionSet |
| SCV002099547.2 (not-provided).jsonc | SCV002099547.2 | not provided (supports) | Not Provided (G.09) | ClinVarNotProvidedProposition, KRAS / Encephalocraniocutaneous lipomatosis |
Oncogenicity (O.10)¶
| File | SCV | Classification | Gene / Condition | Description |
|---|---|---|---|---|
| SCV005093950.2 (onco).json | SCV005093950.2 | Oncogenic (definitive) | ERBB2 / Neoplasm | VariantOncogenicityProposition, CP review status, ClinGen/CGC/VICC Guidelines 2022 method |
Somatic Clinical Impact (S.11-S.14)¶
| File | SCV | Classification | Tier | Sub-type | Description |
|---|---|---|---|---|---|
| SCV004565358.1 (therapeutic-resp-T1).json | SCV004565358.1 | Tier I - Strong | Tier I | Therapeutic Response (S.12) | EGFR L858R / NSCLC, drug sensitivity evidence line with erlotinib therapy, AMP/ASCO/CAP Guidelines 2017 |
| SCV004565361.1 (diagnostic-T2).json | SCV004565361.1 | Tier II - Potential | Tier II | Diagnostic (S.13) | ACVR1 / diffuse intrinsic pontine glioma, diagnostic inclusion criterion evidence line |
| SCV005387955.1 (unk-T3).json | SCV005387955.1 | Tier III - Unknown | Tier III | Clinical Significance (S.11) | TG variant, neutral direction, no paired sub-statement |
| SCV005061369.1 (blb-T4).json | SCV005061369.1 | Tier IV - Benign/LB | Tier IV | Clinical Significance (S.11) | TP53 / CML, disputes direction, no paired sub-statement |
See SCV Statements output reference for field documentation.
VCV Statements¶
Examples of aggregate classification Statement records produced by rolling up SCV submissions through the aggregation hierarchy.
Germline¶
| File | VCV | Prop Types | Submission Levels | Description |
|---|---|---|---|---|
| VCV000012582.63-G-PATH.jsonc | VCV000012582 | Pathogenicity, Association, Not Provided | CP, NOCP, NOCL | Aggregate Contribution Layer germline statement. CP pathogenicity with 13 contributing SCVs concordant, NOCP non-contributing. Association and Not Provided as non-contributing prop types |
Somatic¶
| File | VCV | Prop Types | Tiers | Description |
|---|---|---|---|---|
| VCV000012582.63-S-sci.jsonc | VCV000012582 | Somatic Clinical Impact | Tier I, Tier II | Aggregate Contribution → Priority Grouping → Classification Grouping hierarchy. Priority Grouping combining Tier I and Tier II. CP contributing, NOCP non-contributing |
| VCV000012582.63-S-onco.jsonc | VCV000012582 | Oncogenicity | N/A | Somatic oncogenicity aggregate (Aggregate Contribution → Classification Grouping). Single CP submission, no priority grouping |
PG and EP (single-submission levels)¶
PG (practice guideline) and EP (reviewed by expert panel) submissions are aggregated as separate top-tier submission levels. PG outranks EP in the Aggregate Contribution Layer winner-takes-all selection, followed by CP, NOCP, NOCL, and FLAG.
| File | VCV | Submission Level | Description |
|---|---|---|---|
| VCV-PG-example.jsonc | VCV999999999 (hypothetical) | PG | Classification Grouping statement for a practice guideline submission. Uses standard classification and objectClassification |
| VCV-EP-example.jsonc | VCV999999999 (hypothetical) | EP | Classification Grouping statement for an expert panel submission. Same form as PG; only the submission level qualifier and review status differ |
See VCV Statements output reference for field documentation.