Package | hl7.fhir.uv.genomics-reporting |
Type | StructureDefinition |
Id | Id |
FHIR Version | R4 |
Source | http://hl7.org/fhir/uv/genomics-reporting/https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html |
Url | http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant |
Version | 3.0.0 |
Status | active |
Date | 2024-12-12T20:13:16+00:00 |
Name | Variant |
Title | Variant |
Experimental | False |
Realm | uv |
Authority | hl7 |
Description | Details about a set of changes in the tested sample compared to a reference sequence. |
Copyright | This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc. |
Type | Observation |
Kind | resource |
StructureDefinition | |
http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant | Genomic Variant Profile |
http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-variant | Phenopackets Variant |
http://mitre.org/gdx/StructureDefinition/GdxVariant | GDX Variant |
genomic-report | Genomic Report |
genotype | Genotype |
haplotype | Haplotype |
implication | Genomic Implication |
molecular-biomarker | Molecular Biomarker |
sequence-phase-relationship | Sequence Phase Relationship |
https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/variante | MII PR MolGen Variante |
StructureDefinition | |
finding | Genomic Finding |
repeat-motif-order | Repeat Motif Order |
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs | DNA Change Type |
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | Human Genome Variation Society (HGVS) Nomenclature |
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs | Variant Confidence Status |
Note: links and images are rebased to the (stated) source
Generated Narrative: StructureDefinition variant
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | 0..* | GenomicFinding | Variant | |
code | 1..1 | CodeableConcept | 69548-6 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
Slices for value[x] | 0..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual result Slice: Unordered, Open by type:$this | |
value[x]:valueCodeableConcept | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) | |
method | 0..1 | CodeableConcept | Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible) | |
Slices for component | Content/Rules for all slices | |||
component:representative-coding-hgvs | 0..1 | BackboneElement | DNA change (c.HGVS) | |
code | 1..1 | CodeableConcept | 48004-6 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
value[x] | 1..1 | CodeableConcept | A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T. Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | |
component:genomic-hgvs | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS | |
code | 1..1 | CodeableConcept | 81290-9 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
value[x] | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | |
component:cytogenomic-nomenclature | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) | |
code | 1..1 | CodeableConcept | 81291-7 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |
value[x] | 1..1 | CodeableConcept | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined | |
component:genomic-ref-seq | 0..1 | BackboneElement | Genomic Reference Sequence | |
code | 1..1 | CodeableConcept | 48013-7 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
value[x] | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | |
component:representative-protein-ref-seq | 0..1 | BackboneElement | Protein Reference Sequence | |
code | 1..1 | CodeableConcept | protein-ref-seq Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: protein-ref-seq | |
value[x] | 1..1 | CodeableConcept | Versioned protein reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | |
component:representative-transcript-ref-seq | 0..1 | BackboneElement | Reference Transcript | |
code | 1..1 | CodeableConcept | 51958-7 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
value[x] | 1..1 | CodeableConcept | Versioned transcript reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | |
component:exact-start-end | 0..1 | BackboneElement | Exact Start-End | |
code | 1..1 | CodeableConcept | 81254-5 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81254-5 | |
value[x] | 0..1 | Range | Range in question. 'High' can be omitted for single nucleotide variants. | |
component:inner-start-end | 0..1 | BackboneElement | Inner Start-End | |
code | 1..1 | CodeableConcept | 81302-2 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81302-2 | |
value[x] | 0..1 | Range | Imprecise variant inner-bounding range | |
component:outer-start-end | 0..1 | BackboneElement | Outer Start-End | |
code | 1..1 | CodeableConcept | 81301-4 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81301-4 | |
value[x] | 0..1 | Range | Imprecise variant outer-bounding range | |
component:coordinate-system | 0..1 | BackboneElement | Coordinate System | |
code | 1..1 | CodeableConcept | 92822-6 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |
value[x] | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) | |
component:ref-allele | 0..1 | BackboneElement | Genomic Ref Allele | |
code | 1..1 | CodeableConcept | 69547-8 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |
value[x] | 0..1 | string | Normalized string per the VCF format. | |
component:alt-allele | 0..1 | BackboneElement | Genomic Alt Allele | |
code | 1..1 | CodeableConcept | 69551-0 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |
value[x] | 0..1 | string | Normalized string per the VCF format. | |
component:coding-change-type | 0..1 | BackboneElement | Coding DNA Change Type | |
code | 1..1 | CodeableConcept | 48019-4 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
value[x] | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072 | |
component:genomic-source-class | 0..1 | BackboneElement | Genomic Source Class | |
code | 1..1 | CodeableConcept | 48002-0 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
value[x] | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) | |
component:sample-allelic-frequency | 0..1 | BackboneElement | Sample Allelic Frequency | |
code | 1..1 | CodeableConcept | 81258-6 Required Pattern: At least the following | |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |
value[x] | 0..1 | Quantity | Relative frequency in the sample | |
system |