GeneticVariantDetai
Main variant result table.
| Column Name | Type | Description |
|---|---|---|
| MeetsAmplificationThresholdIndicator | VARCHAR | Indicates whether the copy number variation meets the amplification threshold for this variant. 'Y' indicates that the variant has met the threshold. 'N' indicates that the variant is known to not meet the threshold. NULL might indicate that amplification does not apply, was not resulted, or could not be determined. |
| VariantStartPosition | INTEGER | The position where the variation starts. |
| GenomicReferenceSequenceIdentifier | VARCHAR | The external ID defining the Genomic Reference Sequence. |
| VariantCopyNumberLowerBound | NUMERIC | Lower bound for the copy number of a variant. |
| DnaChangeRelativeToTranscriptReferenceSequence | VARCHAR | The change at the DNA level relative to the Transcript Reference Sequence. |
| PharmacogenomicAdverseReactionRiskPhenotype | INTEGER | Predicted phenotype for risk of adverse drug reaction. |
| VariantNameHGVS | VARCHAR | The HGVS name assigned to the variant. |
| StructuralVariantOuterEndPosition | INTEGER | Structural variant outer end position. |
| VariantCopyNumberUpperBound | NUMERIC | Upper bound for the copy number of a variant. |
| GeneDefiningSourceIdentifier | INTEGER | The category ID corresponding to the source that defined the gene name. |
| PharmacogenomicActivityScoreLowerBound | NUMERIC | The lower bound of the activity score on the pharmacogenomic variant. If the activity score is a value and not a range, this will have the same value as PGX_ACT_SCORE_UPPER. If the activity score is a range without a lower bound specified, this column will contain 0. |
| AssociatedGeneName | VARCHAR | The gene name. |
| StructuralVariantOuterStartPosition | INTEGER | Structural variant outer start position. |
| VariantDisplayName | VARCHAR | The name used when the variant is displayed |
| VariantPresenceAssessmentCategory | INTEGER | The category ID corresponding to the value in LOINC 69548-6, indicating whether the variant is present, absent, indeterminate, or if no call was made. |
| VariantAminoAcidChange | VARCHAR | The change at the amino acid (protein) level caused by the DNA change. |
| ParentalInheritanceCategory | INTEGER | The category ID that defines the parental set(s) of chromosomes a variant was inherited from, if any. If it was not inherited from the tested parent(s) then the category IDs of "De novo", "Not Maternal", or "Not Paternal" are used as appropriate. This field displays to end users as Parental Inheritance. |
| PatientIdentifier | VARCHAR | The unique identifier of the patient associated with the variant. |
| VariantChromosomeCategory | INTEGER | The category ID corresponding to the chromosome the variant is found on. |
| GenomicReferenceSequenceChange | VARCHAR | The change at the DNA level relative to the Genomic Reference Sequence. |
| VariantFunctionalEffectCategory | INTEGER | The category ID for the functional effect of the variant |
| VariantClassificationCategory | INTEGER | The category ID corresponding to the variant's classification. The name of this item was changed from clinical significance to variant classification. It appears as variant classification in end-user facing locations, but the column name remains CLINICAL_SIGNIF_C for backwards compatibility. |
| PersistentPatientIdentifier | VARCHAR | The unique ID of the patient record for this row. This column is frequently used to link to the PATIENT table. While the ID in the PAT_ID column will get cleared out when its variant record is superseded, the value in this column will continue to indicate the patient. |
| GenomicReferenceSequenceSystemCode | INTEGER | The category ID for the source that defined the Genomic Reference Sequence. |
| ChromosomeRegion | VARCHAR | The part of the chromosome in which the variation was found on. |
| VariantAssignedName | VARCHAR | The name assigned to the variant. |
| VariantMolecularConsequenceCategoryIdentifier | INTEGER | The molecular consequence category ID for the variant. |
| VariantCopyNumberInteger | INTEGER | Genomic structural variant copy number as an integer. To prepare for the future deprecation of this column, your content should use either the COPY_NUMBER_LOWER or the COPY_NUMBER_UPPER columns or both. |
| PharmacogenomicActivityScoreUpperBound | NUMERIC | The upper bound of the activity score on the pharmacogenomic variant. If the activity score is a value and not a range, this will have the same value as PGX_ACT_SCORE_LOWER. If the activity score is a range without an upper bound specified, this column will contain 99999. |
| TranscriptReferenceSequenceSourceSystemIdentifier | INTEGER | The category ID for the source that defined the Transcript Reference Sequence. |
| VariantAllelicStateCategoryIdentifier | INTEGER | The allelic state category ID for the variant. |
| IsExternalSourceData | VARCHAR | Indicates whether the variant should be considered external, such as auto-reconciliation by Happy Together using data from an external organization. |
| ObservedAlleleSequence | VARCHAR | The DNA sequence in the test sample (Ref Allele) that is different from the DNA sequence in the reference sequence (Ref Allele). |
| PharmacogenomicDrugTransportPhenotype | INTEGER | Predicted phenotype for drug efficacy through drug transport mechanism. |
| NonParticipatingSubmitterPatientIdentifier | NUMERIC | The unique ID of the non-participating submitter's patient (RQG) associated with the variant. |
| PharmacogenomicDrugMetabolismEffect | INTEGER | Stores effect on drug metabolism for a pharmacogenomic variant. |
| LogicalOwnerCommunityIdentifier | VARCHAR | The Community ID (CID) of the instance from which this record or line was extracted. This is only populated if you use IntraConnect. |
| VariantGeneIdentification | NUMERIC | Gene where the variant is located. |
| VariantVariationTypeCategoricalIdentifier | INTEGER | The type of variation category ID for the variant. |
| VariantGenotypeName | VARCHAR | Genotype Name, used in combination with the column GENE (VAR 1210) to describe a Pharmacogenomic Variant. |
| ProteinReferenceSequenceIdentifier | VARCHAR | The external identifier defining the Protein Reference Sequence. |
| GenomicSourceCategory | INTEGER | The category ID corresponding to the source of the tissue for this variant. |
| TotalRepeatExpansionCount | INTEGER | Total repeat number is the sum of all repeat numbers for one repeat expansion variant. |
| StructuralVariantInnerStartPosition | INTEGER | Structural variant inner start position. |
| StandardizedGenotypeIdentifier | VARCHAR | Returns the genotype (VARIANT.GENOTYPE) converted to a standardized format. Use VARIANT.GENOTYPE for display and VARIANT.GENOTYPE_IDENT for identifying same genotypes regardless of formatting used in VARIANT.GENOTYPE |
| RecordState | INTEGER | Stores the record status (hidden, soft-deleted, etc.). |
| DecimalCopyNumber | NUMERIC | Genomic structural variant copy number with two decimal places of precision. To prepare for the future deprecation of this column, your content should use either the COPY_NUMBER_LOWER or the COPY_NUMBER_UPPER columns or both. |
| PharmacogenomicDrugEfficacyCategory | INTEGER | Predicted phenotype for ability of drug to bind to intended site in order to deliver intended effect. |
| VariantInternationalSystemForCytogenomicNomenclatureName | VARCHAR | The ISCN name assigned to the variant. |
| TranscriptReferenceSequenceIdentifier | VARCHAR | The external identifier defining the Transcript Reference Sequence. |
| VariantDeterminationMethodType | INTEGER | The category ID for the type of method used to determine this variant. |
| VariantPenetranceValue | NUMERIC | The penetrance for the variant. |
| VariantIdentifier | NUMERIC | The unique identifier for the variant record. |
| HistoricRequisitionGrouperIdentifier | NUMERIC | The historically maintained requisition grouper ID. While the requisition grouper ID in item 99 will be cleared out of a VAR record when a new VAR superscedes it, this will retain the grouper link. |
| StructuralVariantInnerEndPosition | INTEGER | Structural variant inner end position. |
| BoundaryPrecisionNarrative | VARCHAR | Structural variant narrative description of the boundary precision. |
| VariantMosaicismCategory | INTEGER | The mosaicism category ID for the variant record as reported by the lab. |
| VariantIncidentalFindingType | INTEGER | Stores whether the variant represents an incidental finding. |
| AllelicPhaseEvidenceBasis | INTEGER | The category ID corresponding to the evidence on which the allelic phase (which displays to end users as parental inheritance) was concluded. This field displays to end users as Basis For Parental Inheritance. |
| GenomeAssemblyCategory | INTEGER | The category ID corresponding to the reference assembly used for analyzing this variant. |
| StructuralVariantAlleleLength | INTEGER | Structural variant allele length. |