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SCV Statements (gks_scv_statement_proc)

Overview

The clinvar_ingest.gks_scv_statement_proc stored procedure transforms ClinVar submitted clinical variant (SCV) data into GA4GH VA-Spec Statement format. It builds complete clinical assertion records from SCV submissions — linking classification codes, propositions, qualifiers, conditions, citations, and submitter metadata into structured statements suitable for downstream aggregation and export.

The procedure accepts two parameters — on_date DATE and debug BOOL — where on_date identifies the ClinVar release schema to process and debug controls diagnostic output.

Workflow

The procedure executes the following steps sequentially within a loop over the target schema(s) identified by the on_date parameter.

Steps produce two types of output:

  • Pipeline table — persists in BigQuery for use by downstream procedures or external processing
  • Internal — exists only within the procedure and is consumed by later steps

Step 1: Build temp_gks_scv

Extracts SCV records from scv_summary and clinical_assertion, joining to clinvar_clinsig_types for classification mapping and submission_level for submission level. Produces the foundational record with proposition type, direction, classification codes, strength, submitter info, drug therapy (for somatic), assertion method attributes, citations, submission_level code and label.

Output: temp_gks_scv — one row per SCV with core classification and submitter metadata. Internal

Step 2: Build temp_gene_context_qualifiers

Extracts gene context qualifiers by joining single-gene variations with submitted gene symbols from clinical_assertion_variation. Produces gene concept records with primaryCoding (NCBI Gene), HGNC mappings, and submittedGeneSymbols extensions.

Output: temp_gene_context_qualifiers — one row per SCV+gene combination. Internal

Step 3: Build temp_moi_qualifiers

Extracts mode of inheritance qualifiers from assertion attributes. Maps to HPO terms when available.

Output: temp_moi_qualifiers — one row per SCV with mode of inheritance. Internal

Step 4: Build temp_penetrance_qualifiers

Builds penetrance qualifiers for low-penetrance and risk allele classifications.

Output: temp_penetrance_qualifiers — one row per SCV with penetrance qualifier. Internal

Step 5: Build temp_gks_scv_proposition

Assembles primary SCV propositions by joining SCV records with gene context, MOI, penetrance qualifiers and condition sets from gks_scv_condition_sets.

Output: temp_gks_scv_proposition — one row per SCV with fully assembled proposition. Internal

Step 6: Build temp_gks_scv_target_proposition

Builds somatic target propositions for clinical impact assertions (prognostic, diagnostic, therapeutic) with drug therapy extraction.

Output: temp_gks_scv_target_proposition — one row per somatic SCV with target proposition. Internal

Step 7: Build gks_dict_scv

Final assembly of VA-Spec Statement records. Joins SCV records with propositions, conditions, citations, and assertion methods. Builds the classification struct with description extension, contributions array, extensions array (clinvarScvId, clinvarScvVersion, clinvarScvReviewStatus, submittedScvClassification, submittedScvLocalKey, submissionLevel), and somatic evidence lines.

Output: gks_dict_scv — one row per SCV with complete VA-Spec Statement record. Pipeline table

Output Tables

Table Description Role
temp_gks_scv Core SCV records with classification and submitter metadata Internal
temp_gene_context_qualifiers Gene context qualifiers with NCBI Gene and HGNC mappings Internal
temp_moi_qualifiers Mode of inheritance qualifiers with HPO term mappings Internal
temp_penetrance_qualifiers Penetrance qualifiers for low-penetrance and risk alleles Internal
temp_gks_scv_proposition Assembled primary propositions with qualifiers and conditions Internal
temp_gks_scv_target_proposition Somatic target propositions for clinical impact assertions Internal
gks_dict_scv Complete VA-Spec Statement records for all SCVs Pipeline table

Dependencies

  • UDFs: clinvar_ingest.parseAttributeSet, clinvar_ingest.parseCitations, clinvar_ingest.parseGeneLists, clinvar_ingest.schema_on, clinvar_ingest.cleanup_temp_tables
  • Source Tables: scv_summary, clinical_assertion, clinical_assertion_variation, single_gene_variation, gene, variation_archive
  • Lookup Tables: clinvar_clinsig_types, submission_level, hpo_terms
  • Upstream Procedures: gks_scv_condition_proc (provides gks_scv_condition_sets), gks_catvar_proc
  • Downstream Consumers: gks_vcv_proc, gks_vcv_statement_proc, gks_json_proc

Detailed Documentation

  • SCV Records — foundational SCV record extraction (Step 1)
  • Propositions — qualifier assembly and proposition construction (Steps 2-6)
  • Final Statements — complete statement assembly (Step 7)

Examples

See SCV statement examples in the repository for annotated JSONC examples covering pathogenicity, oncogenicity, somatic clinical impact, and therapeutic response statement types.