_variant_occurrence
Clinical Data Table - Genomic Variants
Table Columns
| field | type | required | phi | phi scrubbing operation |
|---|---|---|---|---|
| variant_occurrence_id | INT64 | Yes | Yes | Sub Not Stable between Data Refreshes |
| person_id | INT64 | Yes | Yes | Sub with Stable between Data Refreshes |
| visit_occurrence_id | INT64 | No | Yes | Sub with Stable between Data Refreshes |
| procedure_occurrence_id | INT64 | No | Yes | Sub Not Stable between Data Refreshes |
| provider_id | INT64 | No | Yes | Sub with Stable between Data Refreshes |
| order_datetime | DATETIME | No | Yes | Jitter |
| test_name | STRING | No | Whitelist | |
| variant_name | STRING | No | ||
| variant_type | STRING | No | Whitelist | |
| assessment | STRING | No | Whitelist | |
| genome_assembly | STRING | No | Whitelist | |
| chromosome | STRING | No | ||
| transcript_ref_seq | STRING | No | ||
| dna_change | STRING | No | ||
| dna_var_type | STRING | No | Whitelist | |
| amino_acid_change | STRING | No | ||
| variant_molecular_consequence | STRING | No | Whitelist | |
| genomic_dna_change | STRING | No | ||
| allelic_frequency | NUMERIC(18, 5) | No | ||
| copy_number_lower | NUMERIC(9, 2) | No | ||
| copy_number_upper | NUMERIC(9, 2) | No | ||
| gene_name | STRING | No | ||
| phenotype_spec_var_class | STRING | No | Whitelist | |
| interpretation | STRING | No | Yes | TiDE |
| accession_number | STRING | No | Yes | Hash |
| stamp_pipeline_version | STRING | No | Whitelist | |
| specimen_type | STRING | No | Whitelist | |
| specimen_source | STRING | No | Whitelist |
Columns Description
variant_occurrence_id (PK)
This is the primary key of the table. This is a unique identifier for every variant occurrence. It is assumed that every variant occurrence with a different unique identifier is in fact a different event and should be treated independently.
person_id (FK)
A foreign key identifier to the person_id in the person table for whom the condition is recorded.
visit_occurrence_id (FK)
A foreign key identifier to the visit_occurrence_id in the visit_occurrence table for the visit associated with the ordered test.
procedure_occurrence_id (FK)
A foreign key identifier to the OMOP procedure_occurrence table for the procedure order for the variant test.
provider_id (FK)
A foreign key identifier to the provider in the provider table who authorized the order for the variant test.
order_datetime
The datetime when the test was ordered.
test_name
The name of the test associated with the variant record.
variant_name
The name of the genetic variant identified in the test.
variant_type
The variant type, such as ‘Simple’, ‘Pharmacogenomic genotype’, ‘Negative’, etc.
assessment
The assessment of the variant, such as ‘Detected’, ‘Not Detected’, ‘Negative’, etc.
genome_assembly
The genome assembly used for the variant, such as ‘GRCh37’, ‘GRCh38’, ‘hg38’, etc.
chromosome
The chromosome on which the variant is located, such as ‘1’, ‘2’, ‘X’, ‘Y’, etc.
transcript_ref_seq
The external identifier defining the Transcript Reference Sequence.
dna_change
The change at the DNA level relative to the Transcript Reference Sequence.
dna_var_type
The descriptive name for the DNA sequence variation type, such as ‘Substitution’, ‘Copy number gain’, ‘Deletion’, etc.
amino_acid_change
The change at the amino acid (protein) level caused by the DNA change.
variant_molecular_consequence
The descriptive name for the molecular consequence of the variant, such as ‘Missense Variant’, ‘Nonsense’, ‘Frameshift Variant’, etc.
genomic_dna_change
The change at the DNA level relative to the Genomic Reference Sequence.
allelic_frequency
The percentage of all of the reads at this genomic location that were represented by the given allele. For homozygotes it will be close to 100%; for heterozygotes it will be close to 50%. It can be a smaller number when there are mosaics or multiple chromosomes, or mixtures of tumor cells and normal cells. It is stored in the system as a decimal between 0 and 1 - this is calculated by dividing the percentage by 100.
copy_number_lower
The lower bound of the copy number range for the variant.
copy_number_upper
The upper bound of the copy number range for the variant.
gene_name
The name of the gene associated with the variant record, such as ‘POLE’, ‘TP53’, ‘CYP2D6’, etc.
phenotype_spec_var_class
The descriptive name for the phenotype variant class, such as ‘Pathogenic’, ‘Likely Pathogenic’, ‘Uncertain Significance’, etc.
interpretation
The full text interpretation associated with the variant record, aggregated from individual interpretation lines.
accession_number
The specimen accession numbers associated with the ordered test, stored as a comma-separated string if multiple accession numbers are present.
stamp_pipeline_version
The version of the STAMP pipeline used for the test associated with the variant record.
specimen_type
The specimen type associated with the order for the variant record, such as ‘Blood’, ‘Tissue/Bone - Biopsy’, ‘Existing Patient Material’, etc.
specimen_source
The specimen source associated with the order for the variant record, such as ‘Blood, from Venipuncture’, ‘Saliva’, ‘Liver’, etc.