Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Variant

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant Version: 3.0.1-SNAPSHOT
Active as of 2024-07-08 Computable Name: Variant

Copyright/Legal: 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.

Details about a set of changes in the tested sample compared to a reference sequence.

Scope and Usage

This profile allows a full description of the variant found using properties from a variety of testing approaches and allowing for a variety of descriptive mechanisms. Labs are encouraged to populate what properties they know. In future versions of this implementation guide, HL7 may provide additional guidance on what properties should be sent in which situations and may subdivide Variant into multiple sub-profiles with more specific purpose.

Other Guidance

See Variant Reporting for details on use.

If implementers have additional variant annotations, the Variant profile is defined to allow flexibility. See the section on flexibility for additional guidancem, especially the guidance for the Open Slicing allowed on Observation.component.

Usage:

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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)
.... 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: (unbound) (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: (unbound) (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: (unbound) (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: (unbound) (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 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth 0..1 BackboneElement Allelic Read Depth
..... code 1..1 CodeableConcept 82121-5
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: 82121-5
..... value[x] 0..1 Quantity Unfiltered count of supporting reads
.... component:allelic-state 0..1 BackboneElement Allelic State
..... code 1..1 CodeableConcept 53034-5
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: 53034-5
..... value[x] 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance 0..1 BackboneElement Origin of germline genetic variant
..... code 1..1 CodeableConcept 94186-4
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: 94186-4
..... value[x] 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis 0..1 BackboneElement Evidential basis for variant inheritance
..... code 1..1 CodeableConcept Basis for allelic phase
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: 82309-6
..... value[x] 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code 0..* BackboneElement Variation Code
..... code 1..1 CodeableConcept 81252-9
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: 81252-9
..... value[x] 1..1 CodeableConcept ClinVar ID or similar
Binding: (unbound) (example): Multiple bindings acceptable

.... component:chromosome-identifier 0..* BackboneElement Chromosome Identifier
..... code 1..1 CodeableConcept 48000-4
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: 48000-4
..... value[x] 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:representative-protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... code 1..1 CodeableConcept 48005-3
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: 48005-3
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:copy-number 0..1 BackboneElement Genomic Structural Variant Copy Number
..... code 1..1 CodeableConcept 82155-3
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: 82155-3
..... value[x] 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
.... component:variant-confidence-status 0..1 BackboneElement Variant Confidence Status
..... code 1..1 CodeableConcept variant-confidence-status
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: variant-confidence-status
..... value[x] 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif 0..* BackboneElement Repeat Motif
..... Slices for extension Content/Rules for all slices
...... repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... code 1..1 CodeableConcept repeat-motif
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: repeat-motif
..... value[x] 1..1 string CAG
.... component:repeat-number 0..* BackboneElement Repeat Number
..... Slices for extension Content/Rules for all slices
...... repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... code 1..1 CodeableConcept repeat-number
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: repeat-number
..... value[x] 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.value[x]:valueCodeableConceptrequiredLOINC LL1971-2
http://loinc.org/vs/LL1971-2
Observation.methodextensibleLOINC LL4048-6
http://loinc.org/vs/LL4048-6
Observation.component:representative-coding-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:genomic-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:genomic-ref-seq.value[x]example
Observation.component:representative-protein-ref-seq.value[x]example
Observation.component:representative-transcript-ref-seq.value[x]example
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
Observation.component:coding-change-type.value[x]extensibleDNAChangeTypeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs
from this IG
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
http://loinc.org/vs/LL378-1
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
http://loinc.org/vs/LL381-5
Observation.component:variant-inheritance.value[x]extensibleLOINC LL5489-1
http://loinc.org/vs/LL5489-1
Observation.component:variant-inheritance-basis.value[x]extensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2
Observation.component:variation-code.value[x]example
Observation.component:chromosome-identifier.value[x]requiredLOINC LL2938-0
http://loinc.org/vs/LL2938-0
Observation.component:representative-protein-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:variant-confidence-status.value[x]requiredVariantConfidenceStatusVS (a valid code from Variant Confidence Status Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs
from this IG
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicFinding Variant
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


.... body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
.... category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
... code Σ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] ΣC 0..1 Actual result
Slice: Unordered, Open by type:$this
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
.... value[x]:valueCodeableConcept ΣC 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)
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
... Slices for component Σ 0..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: conclusion-string
.... component:gene-studied Σ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48018-6
..... value[x] Σ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
.... component:cytogenetic-location Σ 0..* BackboneElement Cytogenetic (Chromosome) Location
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48001-2
..... value[x] Σ 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly Σ 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 62374-4
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:representative-coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 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 Σ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 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 Σ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 1..1 CodeableConcept Actual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:representative-protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:representative-transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
.... component:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 0..1 Range Imprecise variant inner-bounding range
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 0..1 Range Imprecise variant outer-bounding range
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 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 Σ 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 0..1 string Normalized string per the VCF format.
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 0..1 string Normalized string per the VCF format.
.... component:coding-change-type Σ 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 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 Σ 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 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 Σ 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] Σ 0..1 Quantity Relative frequency in the sample
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 82121-5
..... value[x] Σ 0..1 Quantity Unfiltered count of supporting reads
.... component:allelic-state Σ 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 53034-5
..... value[x] Σ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ 0..1 BackboneElement Origin of germline genetic variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 94186-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 94186-4
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis Σ 0..1 BackboneElement Evidential basis for variant inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Basis for allelic phase
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 82309-6
..... value[x] Σ 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code Σ 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 81252-9
..... value[x] Σ 1..1 CodeableConcept ClinVar ID or similar
Binding: (unbound) (example): Multiple bindings acceptable

.... component:chromosome-identifier Σ 0..* BackboneElement Chromosome Identifier
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48000-4
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:representative-protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48005-3
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:copy-number Σ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 82155-3
..... value[x] Σ 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
.... component:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: variant-confidence-status
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif Σ 0..* BackboneElement Repeat Motif
..... Slices for extension Content/Rules for all slices
...... repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-motif
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: repeat-motif
..... value[x] Σ 1..1 string CAG
.... component:repeat-number Σ 0..* BackboneElement Repeat Number
..... Slices for extension Content/Rules for all slices
...... repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-number
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: repeat-number
..... value[x] Σ 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexamplePattern: LOINC Code 69548-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.value[x]:valueCodeableConceptrequiredLOINC LL1971-2
http://loinc.org/vs/LL1971-2
Observation.methodextensibleLOINC LL4048-6
http://loinc.org/vs/LL4048-6
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:cytogenetic-location.codeexamplePattern: LOINC Code 48001-2
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC Code 62374-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
http://loinc.org/vs/LL1040-6
Observation.component:representative-coding-hgvs.codeexamplePattern: LOINC Code 48004-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:representative-coding-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:genomic-hgvs.codeexamplePattern: LOINC Code 81290-9
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:genomic-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC Code 81291-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC Code 48013-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:genomic-ref-seq.value[x]example
Observation.component:representative-protein-ref-seq.codeexamplePattern: protein-ref-seq
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:representative-protein-ref-seq.value[x]example
Observation.component:representative-transcript-ref-seq.codeexamplePattern: LOINC Code 51958-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:representative-transcript-ref-seq.value[x]example
Observation.component:exact-start-end.codeexamplePattern: LOINC Code 81254-5
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:inner-start-end.codeexamplePattern: LOINC Code 81302-2
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:outer-start-end.codeexamplePattern: LOINC Code 81301-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:coordinate-system.codeexamplePattern: LOINC Code 92822-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
Observation.component:ref-allele.codeexamplePattern: LOINC Code 69547-8
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:alt-allele.codeexamplePattern: LOINC Code 69551-0
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:coding-change-type.codeexamplePattern: LOINC Code 48019-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:coding-change-type.value[x]extensibleDNAChangeTypeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs
from this IG
Observation.component:genomic-source-class.codeexamplePattern: LOINC Code 48002-0
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
http://loinc.org/vs/LL378-1
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC Code 81258-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
http://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1
from the FHIR Standard
Observation.component:allelic-read-depth.codeexamplePattern: LOINC Code 82121-5
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:allelic-state.codeexamplePattern: LOINC Code 53034-5
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
http://loinc.org/vs/LL381-5
Observation.component:variant-inheritance.codeexamplePattern: LOINC Code 94186-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:variant-inheritance.value[x]extensibleLOINC LL5489-1
http://loinc.org/vs/LL5489-1
Observation.component:variant-inheritance-basis.codeexamplePattern: LOINC Code 82309-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:variant-inheritance-basis.value[x]extensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2
Observation.component:variation-code.codeexamplePattern: LOINC Code 81252-9
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:variation-code.value[x]example
Observation.component:chromosome-identifier.codeexamplePattern: LOINC Code 48000-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:chromosome-identifier.value[x]requiredLOINC LL2938-0
http://loinc.org/vs/LL2938-0
Observation.component:representative-protein-hgvs.codeexamplePattern: LOINC Code 48005-3
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:representative-protein-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:copy-number.codeexamplePattern: LOINC Code 82155-3
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:variant-confidence-status.codeexamplePattern: variant-confidence-status
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:variant-confidence-status.value[x]requiredVariantConfidenceStatusVS (a valid code from Variant Confidence Status Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs
from this IG
Observation.component:repeat-motif.codeexamplePattern: repeat-motif
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:repeat-number.codeexamplePattern: repeat-number
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorObservationIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicFinding Variant
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by pattern:url
.... secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


.... body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
... status ?!Σ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
.... category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version