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Sequence Locations (variation_loc)

Overview

The variation_loc table is created by the clinvar_ingest.variation_identity stored procedure. It extracts and normalizes sequence location data from ClinVar variation records, deriving both gnomAD-formatted identifiers and HGVS expressions from the positional coordinates provided in each variant's Location element. Each row represents a single sequence location for a given variation on a specific accession.

Fields

Field Type Description
variation_id string ClinVar variation identifier.
variation_type string The type of variation as classified by ClinVar (e.g., single nucleotide variant, Deletion, Duplication, copy number gain, copy number loss). Carried forward from the source variation record.
accession string The sequence accession (e.g., NC_000001.11) on which this location is defined. Only locations with a non-null accession are included.
assembly string The genome assembly name (e.g., GRCh38, GRCh37).
assembly_version int64 Numeric assembly build number extracted from the assembly string (e.g., 38, 37).
chr string The chromosome identifier (e.g., 1, X, MT). Locations where chr is Un (unknown) have their gnomad_source set to NULL.
start int64 Precise start position on the sequence (0-based or 1-based per ClinVar convention). NULL for locations that only have inner/outer range endpoints.
stop int64 Precise stop position on the sequence. NULL for locations that only have inner/outer range endpoints.
inner_start int64 Inner start position for imprecise structural variant locations.
inner_stop int64 Inner stop position for imprecise structural variant locations.
outer_start int64 Outer start position for imprecise structural variant locations.
outer_stop int64 Outer stop position for imprecise structural variant locations.
variant_length int64 The variant length as explicitly reported by ClinVar in the location element. May be NULL.
position_vcf int64 VCF-style position for the variant.
reference_allele_vcf string VCF-style reference allele.
alternate_allele_vcf string VCF-style alternate allele.
gnomad_source string A gnomAD-formatted variant identifier derived from VCF fields, in the format chr-position_vcf-ref-alt (e.g., 1-12345-A-G). NULL when any required component is missing or when the chromosome is Un.
loc_hgvs_source string An HGVS expression derived from the location's positional data using the clinvar_ingest.deriveHGVS function. Only populated when an accession is present. This provides a fallback HGVS expression for variants that lack one in the HGVS list.
loc_hgvs_issue string A pre-identified issue with the derived loc_hgvs_source expression. Currently flags accessions with prefixes not supported by vrs-python. NULL when no issue is detected.
varlen_precedence int64 Assembly-based precedence rank for variant length derivation: 1 = GRCh38, 2 = GRCh37, 3 = GRCh36. Used when choosing the best length estimate across assemblies.
has_range_endpoints boolean Whether any inner/outer range endpoint is present (i.e., the location uses imprecise coordinates rather than exact start/stop).
derived_variant_length int64 Variant length calculated from available positional data. Uses variant_length if provided, otherwise falls back to stop - start, then inner_stop - inner_start, then outer_stop - outer_start.
derived_start string A string representation of the start position. For precise locations this is the start value as a string. For imprecise locations it is formatted as [outer_start, inner_start] with nulls shown as null.
derived_stop string A string representation of the stop position. For precise locations this is the stop value as a string. For imprecise locations it is formatted as [inner_stop, outer_stop] with nulls shown as null.

Row Granularity

One row per variation_id + accession + assembly combination. A single variation may have multiple rows when ClinVar provides locations on multiple assemblies (e.g., GRCh38 and GRCh37) or on multiple accessions (e.g., chromosomal and alternate loci). Only locations with a non-null accession are included.

Notes

The gnomad_source and loc_hgvs_source fields are complementary derivations from the same positional data. The gnomad_source is available for simple variants with VCF-style representation, while loc_hgvs_source is derived for all variants with an accession. During expression source consolidation, the loc_hgvs_source is only used as a fallback when gnomad_source is not available (see Precedence Hierarchy).