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-G-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-G-ASSOC.jsonc | SCV004035006.2 | association (supports) | Association (G.06) | ClinVarAssociationProposition, KRAS variant with multiple endometrial conditions in a ConditionSet |
| SCV002099547.2-G-NP.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-S-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-S-SCI-T1-TR.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-S-SCI-T2-DIAG.json | SCV004565361.1 | Tier II - Potential | Tier II | Diagnostic (S.13) | ACVR1 / diffuse intrinsic pontine glioma, diagnostic inclusion criterion evidence line |
| SCV005387955.1-S-SCI-T3-VUS.json | SCV005387955.1 | Tier III - Unknown | Tier III | Clinical Significance (S.11) | TG variant, neutral direction, no paired sub-statement |
| SCV005061369.1-S-SCI-T4-BLB.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. The top statement's proposition and direct references are inlined; nested statements and SCVs remain #/ references into the bundle.
Germline¶
| File | VCV | Prop Type | Submission Levels | Description |
|---|---|---|---|---|
| VCV000012582.69-G-PATH.jsonc | VCV000012582 | Pathogenicity | CP, NOCP | Pathogenic/Likely pathogenic. CP contributing with 15 concordant SCVs; NOCP non-contributing with 20 SCVs. The proposition object is an OR condition set of 8 conditions minted for the aggregate |
| VCV000012582.69-G-ASSOC.jsonc | VCV000012582 | Association | NOCP | Single NOCP submission; the object is a ClinVar trait set (AND) of two conditions |
| VCV000012582.69-G-NP.jsonc | VCV000012582 | Not Provided | NOCL | Single NOCL submission for Encephalocraniocutaneous lipomatosis |
| VCV000007105.213-G-PATH.jsonc | VCV000007105 | Pathogenicity | PG, EP, CP, NOCP | Pathogenic, practice guideline. PG contributing (1 SCV); EP (1 SCV), CP (82 SCVs) and NOCP (10 SCVs) non-contributing. Cystic fibrosis |
| VCV000007105.213-G-DR.jsonc | VCV000007105 | Drug Response | EP | Two expert-panel SCVs; the object is an OR condition set of two drug-response conditions |
| VCV000007105.213-G-RF.jsonc | VCV000007105 | Risk Factor | NOCP | Single NOCP submission for a bronchiectasis modifier condition |
| VCV000007105.213-G-NP.jsonc | VCV000007105 | Not Provided | NOCL | Four NOCL SCVs; the object is an OR condition set of three conditions |
Somatic¶
| File | VCV | Prop Type | Tiers | Description |
|---|---|---|---|---|
| VCV000012582.69-S-SCI.jsonc | VCV000012582 | Somatic Clinical Impact | Tier I, Tier II | Aggregate Contribution → Priority Grouping → Classification Grouping hierarchy. CP Priority Grouping combines Tier I (7 SCVs) and Tier II (3 SCVs) and contributes; NOCP (Tier I, 1 SCV) is non-contributing |
| VCV000012582.69-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. VCV000007105.213-G-PATH shows a PG winner with EP, CP and NOCP non-contributing; VCV000007105.213-G-DR shows an EP-only aggregate.
See VCV Statements output reference for field documentation.
RCV Statements¶
Examples of RCV Statement records: the aggregate for one variant and one condition (or condition set), built with the same layers as VCV statements.
Germline¶
| File | RCV | Variant | Prop Type | Condition | Description |
|---|---|---|---|---|---|
| RCV000007523.119-G-PATH.jsonc | RCV000007523 | Variation 7105 | Pathogenicity | Cystic fibrosis | PG contributing (1 SCV); EP (1), CP (44) and NOCP (4) non-contributing |
| RCV000007523.119-G-NP.jsonc | RCV000007523 | Variation 7105 | Not Provided | Cystic fibrosis | NOCL, 2 SCVs |
| RCV001787370.11-G-DR.jsonc | RCV001787370 | Variation 7105 | Drug Response | ivacaftor / lumacaftor response - Efficacy | EP, 1 SCV |
| RCV001787371.11-G-DR.jsonc | RCV001787371 | Variation 7105 | Drug Response | ivacaftor / tezacaftor response - Efficacy | EP, 1 SCV |
| RCV000029215.25-G-PATH.jsonc | RCV000029215 | KRAS (variation 12582) | Pathogenicity | Linear nevus sebaceous syndrome | CP contributing (4 SCVs); NOCP non-contributing (1) |
| RCV000272938.40-G-PATH.jsonc | RCV000272938 | KRAS (variation 12582) | Pathogenicity | not provided | CP contributing (4 SCVs); NOCP non-contributing (1) |
| RCV000548006.14-G-PATH.jsonc | RCV000548006 | KRAS (variation 12582) | Pathogenicity | RASopathy | CP, 2 SCVs |
| RCV000585796.12-G-PATH.jsonc | RCV000585796 | KRAS (variation 12582) | Pathogenicity | Cerebral arteriovenous malformation | CP contributing (1 SCV); NOCP non-contributing (2) |
| RCV004018620.1-G-PATH.jsonc | RCV004018620 | KRAS (variation 12582) | Pathogenicity | Cardiovascular phenotype | Likely pathogenic, CP, 1 SCV |
| RCV004554600.1-G-PATH.jsonc | RCV004554600 | KRAS (variation 12582) | Pathogenicity | Congenital Pulmonary Airway Malformations | CP, 1 SCV |
| RCV005007840.1-G-PATH.jsonc | RCV005007840 | KRAS (variation 12582) | Pathogenicity | ClinVar trait set of 12 conditions (AND) |
CP, 1 SCV; the object is a #/conditionSet/ reference |
| RCV003327361.6-G-ASSOC.jsonc | RCV003327361 | KRAS (variation 12582) | Association | ClinVar trait set of 2 conditions (AND) |
NOCP, 1 SCV |
| RCV001839445.10-G-NP.jsonc | RCV001839445 | KRAS (variation 12582) | Not Provided | Encephalocraniocutaneous lipomatosis | NOCL, 1 SCV |
| RCV001781420.15-G-PATH.jsonc | RCV001781420 | Variation 97850 | Pathogenicity | Inflammatory bowel disease 1 | Conflicting classifications of pathogenicity, CP, 2 SCVs; neutral direction |
Somatic¶
| File | RCV | Variant | Prop Type | Condition | Description |
|---|---|---|---|---|---|
| RCV004668724.2-S-ONCO.jsonc | RCV004668724 | KRAS (variation 12582) | Oncogenicity | Neoplasm | Oncogenic, CP, 1 SCV |
| RCV006253518.1-S-SCI.jsonc | RCV006253518 | KRAS (variation 12582) | Somatic Clinical Impact | Precursor B-cell acute lymphoblastic leukemia | Tier I diagnostic, CP, 1 SCV |
| RCV006253519.1-S-SCI.jsonc | RCV006253519 | KRAS (variation 12582) | Somatic Clinical Impact | Papillary thyroid carcinoma | Tier I diagnostic, CP, 1 SCV |
| RCV006253521.1-S-SCI.jsonc | RCV006253521 | KRAS (variation 12582) | Somatic Clinical Impact | Glioma | Tier I diagnostic, CP, 1 SCV |
| RCV006253522.1-S-SCI.jsonc | RCV006253522 | KRAS (variation 12582) | Somatic Clinical Impact | Embryonal rhabdomyosarcoma | Tier I diagnostic, CP, 1 SCV |
| RCV006253523.1-S-SCI.jsonc | RCV006253523 | KRAS (variation 12582) | Somatic Clinical Impact | Diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtype | Tier I diagnostic, CP, 1 SCV |
| RCV006253525.1-S-SCI.jsonc | RCV006253525 | KRAS (variation 12582) | Somatic Clinical Impact | Adenocarcinoma of the large intestine | Tier I diagnostic, CP, 1 SCV |
| RCV006253527.1-S-SCI.jsonc | RCV006253527 | KRAS (variation 12582) | Somatic Clinical Impact | Ovarian mucinous adenocarcinoma | Tier I diagnostic, CP, 1 SCV |
| RCV006254391.1-S-SCI.jsonc | RCV006254391 | Variation 2758242 | Somatic Clinical Impact | Medulloblastoma WNT activated | Tier I diagnostic, CP, 1 SCV |
The somatic clinical impact RCVs follow the Aggregate Contribution → Priority Grouping → Classification Grouping hierarchy (-CP → -CP-T1).
See RCV Statements output reference for field documentation.