Molecular Consequence Use Case

A given variant can have multiple transcript-specific predicted molecular consequences. Clinical applications such as rare disease variant discovery, clinical trial matching, and the determination of therapeutic options for cancer patients may need to examine each predicted consequence as part of a variant filtration and prioritization process.

Detailed Example

In this example, a variant in a gene with multiple transcripts is annotated with multiple transcript-specific molecular consequence predictions. This figure shows multiple transcripts of the ODF2L gene.

This next figure shows a VCF row. A variant in the ODF2L gene has been annotated with the snpEff/snpSIFT variant prediction tool. Things to note include:

• The example here prefixes the URI with http://example.org as is the standard approach in HL7 guides when a code system is not an official terminology
• snpEff predicts a molecular consequence for each known transcript
• Each molecular consequence has one or more 'effects' (drawn from Sequence Ontology), and an 'impact category' (HIGH, MODERATE, LOW, MODIFIER)
• Note how variants occurring outside of exons in certain transcripts (e.g. intron_variant) do not have an associated pHGVS
• snpEff may assign an overall 'LOF' (Loss of Function) prediction. (In these examples, we include the 'LOF' where effect=HIGH)
• This example uses snpSIFT with gnomAD to annotate a population allele frequency
• In some cases, snpEff will assign more than one molecular consequence to a given transcript (e.g. splice_donor_variant&intron_variant)

These following examples correspond to the annotated VCF row.

• Variant (includes population allele frequency)
• Molecular consequence 1 (includes LOF prediction)
• Molecular consequence 2
• Molecular consequence 3
• Molecular consequence 4### evidence-level versus clinical-significance

See Genomic Implication for guidance.

Differentiating AND vs OR

There are several cases where it is necessary to differentiate 'AND' conditions (e.g. a consequence of a DNA variant is both X and Y, as in the first example above where a consequence is both a 'splice_donor_variation' AND a 'intron_variant') vs. 'OR' conditions (e.g. a consequence of a DNA variant may be X or may by Y, as in the example above where a consequence might be 'synonymous variant' OR 'intron_variant'). This situation is not unique to molecular consequences, and arises elsewhere within FHIR (e.g. FHIR Search) and outside of FHIR (e.g. Clinvar submission API condition set). To be consistent with other precedents, where molecular consequences have fields with cardinality >1, the inclusion of multiple values within a field shall indicate an 'AND' condition. An 'OR' condition is represented by multiple observation instances.

See Genomic Implication for additional information. Implication fields affected by this guidance include: derivedFrom, evidence-level, feature-consequence.

• Key Elements Table
• Differential Table
• Snapshot Table
• Statistics/References
• All

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicImplication	Molecular Consequence Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
contained		0..*	Resource	Contained, inline Resources
Slices for extension				Content/Rules for all slices
extension: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.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	1..1	code	registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained 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.
coding		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
category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding		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
code	ΣC	1..1	CodeableConcept	molecular-consequence 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: molecular-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
focus	?!Σ	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
dataAbsentReason	C	0..1	CodeableConcept	Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Slices for derivedFrom	Σ	1..*	Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy)	Related resource from which the observation is made Slice: Unordered, Open by profile:resolve()
derivedFrom:variant	Σ	0..*	Reference(Variant)	Variant the implication is derived from
derivedFrom:genotype	Σ	0..*	Reference(Genotype)	Genotype the implication is derived from
derivedFrom:haplotype	Σ	0..*	Reference(Haplotype)	Haplotype the implication is derived from
derivedFrom:biomarker	Σ	0..*	Reference(Molecular Biomarker)	MolecularBiomarker the implication is derived from
Slices for component	ΣC	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
component:All Slices				Content/Rules for all slices
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	ΣC	0..1	BackboneElement	Clinical Conclusion
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	conclusion-string 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:evidence-level	ΣC	0..*	BackboneElement	Level of Evidence
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	93044-6 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 93044-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar
component:clinical-significance	ΣC	0..1	BackboneElement	Clinical significance
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	53037-8 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 53037-8
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
component:knowledge-base	ΣC	0..1	BackboneElement	Knowledge Base
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	knowledge-base 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: knowledge-base
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Actual component result Binding: Knowledge Base Version Codes (example)
component:annotation-pipeline	ΣC	0..1	BackboneElement	Annotation Pipeline
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	annotation-pipeline 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: annotation-pipeline
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Actual component result
component:coding-hgvs	ΣC	0..1	BackboneElement	DNA change (c.HGVS)
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	48004-6 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48004-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	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:transcript-ref-seq	ΣC	0..1	BackboneElement	Reference Transcript
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	51958-7 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 51958-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Versioned transcript reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
component:protein-hgvs	ΣC	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	48005-3 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48005-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	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:protein-ref-seq	ΣC	0..1	BackboneElement	Protein Reference Sequence
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	protein-ref-seq 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: protein-ref-seq
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Versioned protein reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
component:feature-consequence	ΣC	0..*	BackboneElement	Feature Consequence
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	feature-consequence 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: feature-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
component:functional-effect	ΣC	0..1	BackboneElement	Functional Effect
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	functional-effect 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: functional-effect
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more) Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	Observation Status	📍6.0.0-ballot3	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:evidence-level.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:evidence-level.​value[x]	Base	example	Evidence Level Examples	📦4.0.0-ballot	This IG
Observation.component:clinical-significance.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:clinical-significance.​value[x]	Base	example	​ LOINC Answer Codes for LL4034-6 (missing link)	📦	unknown?
Observation.component:knowledge-base.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:knowledge-base.​value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-ballot	This IG
Observation.component:annotation-pipeline.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:coding-hgvs.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦4.0.0-ballot	This IG
Observation.component:transcript-ref-seq.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not Stated	Unknown
Observation.component:protein-hgvs.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦4.0.0-ballot	This IG
Observation.component:protein-ref-seq.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-ref-seq.​value[x]	Base	example		Not Stated	Unknown
Observation.component:feature-consequence.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:feature-consequence.​value[x]	Base	extensible	Molecular Consequence Value Set	📦4.0.0-ballot	This IG
Observation.component:functional-effect.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:functional-effect.​value[x]	Base	extensible	Functional Effect Value Set	📦4.0.0-ballot	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Observation	If 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If 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-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both	extension.exists() != value.exists()
obs-6	error	Observation	Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value).	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8	error	Observation	bodyStructure SHALL only be present if Observation.bodySite is not present	bodySite.exists() implies bodyStructure.empty()
obs-10	error	Observation	Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present	component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11	error	Observation	if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present	(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

This structure is derived from GenomicImplication

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation		0..*	GenomicImplication	Molecular Consequence
code		1..1	CodeableConcept	molecular-consequence 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: molecular-consequence
Slices for component				Content/Rules for all slices
component:coding-hgvs		0..1	BackboneElement	DNA change (c.HGVS)
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource
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:transcript-ref-seq		0..1	BackboneElement	Reference Transcript
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource
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: (example): Multiple bindings acceptable (NCBI or LRG)
component:protein-hgvs		0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource
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:protein-ref-seq		0..1	BackboneElement	Protein Reference Sequence
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource
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: (example): Multiple bindings acceptable (NCBI or LRG)
component:feature-consequence		0..*	BackboneElement	Feature Consequence
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource
code		1..1	CodeableConcept	feature-consequence 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: feature-consequence
value[x]		1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
component:functional-effect		0..1	BackboneElement	Functional Effect
Slices for extension				Content/Rules for all slices
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource
code		1..1	CodeableConcept	functional-effect 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: functional-effect
value[x]		1..1	CodeableConcept	gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more) Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦4.0.0-ballot	This IG
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not Stated	Unknown
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦4.0.0-ballot	This IG
Observation.component:protein-ref-seq.​value[x]	Base	example		Not Stated	Unknown
Observation.component:feature-consequence.​value[x]	Base	extensible	Molecular Consequence Value Set	📦4.0.0-ballot	This IG
Observation.component:functional-effect.​value[x]	Base	extensible	Functional Effect Value Set	📦4.0.0-ballot	This IG

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicImplication	Molecular Consequence Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
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: AllLanguages (required): IETF language tag for a human language Additional Bindings Purpose CommonLanguages Starter
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension: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.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
instantiates[x]	Σ	0..1	canonical(ObservationDefinition), Reference(ObservationDefinition)	Instantiates FHIR ObservationDefinition
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
triggeredBy		0..*	BackboneElement	Triggering observation(s)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
observation	Σ	1..1	Reference(Observation)	Triggering observation
type	Σ	1..1	code	reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation.
reason		0..1	string	Reason that the observation was triggered
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy)	Part of referenced event
status	?!Σ	1..1	code	registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained 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	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding		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		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	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding		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		0..1	string	Plain text representation of the concept
code	ΣC	1..1	CodeableConcept	molecular-consequence 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: molecular-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	Σ	0..1	Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct)	Who and/or what the observation is about
focus	?!Σ	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
organizer	ΣC	0..1	boolean	This observation organizes/groups a set of sub-observations
encounter	Σ	0..1	Reference(Encounter)	Healthcare event during which this observation is made
effective[x]	Σ	0..1		Clinically relevant time/time-period for observation
effectiveDateTime			dateTime
effectivePeriod			Period
effectiveTiming			Timing
effectiveInstant			instant
issued	Σ	0..1	instant	Date/Time this version was made available
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService)	Who is responsible for the observation
dataAbsentReason	C	0..1	CodeableConcept	Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
bodySite	C	0..1	CodeableConcept	Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
bodyStructure	C	0..1	Reference(BodyStructure)	Observed body structure
method		0..1	CodeableConcept	How it was done Binding: ObservationMethods (example): Methods for simple observations.
specimen	C	0..1	Reference(Specimen | Group)	Specimen used for this observation Constraints: obs-9
device		0..1	Reference(Device | DeviceMetric)	A reference to the device that generates the measurements or the device settings for the device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation Constraints: obs-3
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
low	C	0..1	SimpleQuantity(6.0.0-ballot3)	Low Range, if relevant
high	C	0..1	SimpleQuantity(6.0.0-ballot3)	High Range, if relevant
normalValue		0..1	CodeableConcept	Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation.
type		0..1	CodeableConcept	Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo		0..*	CodeableConcept	Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age		0..1	Range	Applicable age range, if relevant
text	C	0..1	markdown	Text based reference range in an observation
hasMember	Σ	0..*	Reference(Observation | QuestionnaireResponse | MolecularSequence)	Related resource that belongs to the Observation group
Slices for derivedFrom	Σ	1..*	Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy)	Related resource from which the observation is made Slice: Unordered, Open by profile:resolve()
derivedFrom:variant	Σ	0..*	Reference(Variant)	Variant the implication is derived from
derivedFrom:genotype	Σ	0..*	Reference(Genotype)	Genotype the implication is derived from
derivedFrom:haplotype	Σ	0..*	Reference(Haplotype)	Haplotype the implication is derived from
derivedFrom:biomarker	Σ	0..*	Reference(Molecular Biomarker)	MolecularBiomarker the implication is derived from
Slices for component	ΣC	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
component:All Slices				Content/Rules for all slices
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	ΣC	0..1		Actual component result
valueQuantity			Quantity
valueCodeableConcept			CodeableConcept
valueString			string
valueBoolean			boolean
valueInteger			integer
valueRange			Range
valueRatio			Ratio
valueSampledData			SampledData
valueTime			time
valueDateTime			dateTime
valuePeriod			Period
valueAttachment			Attachment
valueReference			Reference(MolecularSequence)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:conclusion-string	ΣC	0..1	BackboneElement	Clinical Conclusion
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	conclusion-string 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:evidence-level	ΣC	0..*	BackboneElement	Level of Evidence
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	93044-6 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 93044-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:clinical-significance	ΣC	0..1	BackboneElement	Clinical significance
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	53037-8 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 53037-8
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:knowledge-base	ΣC	0..1	BackboneElement	Knowledge Base
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	knowledge-base 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: knowledge-base
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Actual component result Binding: Knowledge Base Version Codes (example)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:annotation-pipeline	ΣC	0..1	BackboneElement	Annotation Pipeline
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	annotation-pipeline 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: annotation-pipeline
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:coding-hgvs	ΣC	0..1	BackboneElement	DNA change (c.HGVS)
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	48004-6 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48004-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	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)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:transcript-ref-seq	ΣC	0..1	BackboneElement	Reference Transcript
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	51958-7 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 51958-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Versioned transcript reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:protein-hgvs	ΣC	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	48005-3 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		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48005-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:protein-ref-seq	ΣC	0..1	BackboneElement	Protein Reference Sequence
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	protein-ref-seq 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: protein-ref-seq
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	Versioned protein reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:feature-consequence	ΣC	0..*	BackboneElement	Feature Consequence
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	feature-consequence 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: feature-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
component:functional-effect	ΣC	0..1	BackboneElement	Functional Effect
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	functional-effect 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: functional-effect
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	ΣC	1..1	CodeableConcept	gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more) Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result value
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.language	Base	required	All Languages	📍6.0.0-ballot3	FHIR Std.
Observation.triggeredBy.​type	Base	required	triggered Bytype	📍6.0.0-ballot3	FHIR Std.
Observation.status	Base	required	Observation Status	📍6.0.0-ballot3	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📍6.0.0-ballot3	FHIR Std.
Observation.method	Base	example	Observation Methods	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​normalValue	Base	extensible	Observation Reference Range Normal Value Codes	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​type	Base	preferred	Observation Reference Range Meaning Codes	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​appliesTo	Base	example	Observation Reference Range Applies To Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:evidence-level.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:evidence-level.​value[x]	Base	example	Evidence Level Examples	📦4.0.0-ballot	This IG
Observation.component:evidence-level.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:evidence-level.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:clinical-significance.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:clinical-significance.​value[x]	Base	example	​ LOINC Answer Codes for LL4034-6 (missing link)	📦	unknown?
Observation.component:clinical-significance.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:clinical-significance.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:knowledge-base.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:knowledge-base.​value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-ballot	This IG
Observation.component:knowledge-base.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:knowledge-base.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:annotation-pipeline.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:annotation-pipeline.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:annotation-pipeline.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:coding-hgvs.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦4.0.0-ballot	This IG
Observation.component:coding-hgvs.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:coding-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:transcript-ref-seq.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not Stated	Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:transcript-ref-seq.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-hgvs.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦4.0.0-ballot	This IG
Observation.component:protein-hgvs.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-ref-seq.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-ref-seq.​value[x]	Base	example		Not Stated	Unknown
Observation.component:protein-ref-seq.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:protein-ref-seq.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:feature-consequence.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:feature-consequence.​value[x]	Base	extensible	Molecular Consequence Value Set	📦4.0.0-ballot	This IG
Observation.component:feature-consequence.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:feature-consequence.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:functional-effect.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:functional-effect.​value[x]	Base	extensible	Functional Effect Value Set	📦4.0.0-ballot	This IG
Observation.component:functional-effect.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:functional-effect.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Observation	If 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If 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-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both	extension.exists() != value.exists()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text	low.exists() or high.exists() or text.exists()
obs-6	error	Observation	Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value).	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8	error	Observation	bodyStructure SHALL only be present if Observation.bodySite is not present	bodySite.exists() implies bodyStructure.empty()
obs-9	error	Observation.specimen	If Observation.specimen is a reference to Group, the group can only have specimens	(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
obs-10	error	Observation	Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present	component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11	error	Observation	if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present	(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())