| Name | Flags | Card. | Type |
Description & Constraints
|
|---|---|---|---|---|
Observation
|
GenomicFinding | Variant | ||
code
|
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]
|
Slice: Unordered, Open by type:$this | |||
value[x]:valueCodeableConcept
|
0..1 | CodeableConcept |
Indeterminate | No call | Present | Absent. Binding: todo ( required ) |
|
|
method
|
Sequencing | SNP array | PCR | Computational analysis | ... Binding: todo ( extensible ) |
|||
|
component:representative-coding-hgvs
|
0..1 | DNA change (c.HGVS) | ||
code
|
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.. | 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 | Genomic (gDNA) Change - gHGVS | ||
|
code
|
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.. | 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 | Cytogenomic Nomenclature (ISCN) | ||
|
code
|
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.. | CodeableConcept |
Binding:
todo
( example
): Binding not yet defined |
|
|
component:genomic-ref-seq
|
0..1 | Genomic Reference Sequence | ||
|
code
|
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.. | CodeableConcept |
Versioned genomic reference sequence identifier Binding: todo ( example ): Multiple bindings acceptable (NCBI or LRG) |
|
|
component:representative-transcript-ref-seq
|
0..1 | Reference Transcript | ||
|
code
|
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.. | CodeableConcept |
Versioned transcript reference sequence identifier Binding: todo ( example ): Multiple bindings acceptable (NCBI or LRG) |
|
|
component:exact-start-end
|
0..1 | Exact Start-End | ||
|
code
|
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]
|
Range | Range in question. 'High' can be omitted for single nucleotide variants. | ||
|
component:inner-start-end
|
0..1 | Inner Start-End | ||
|
code
|
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]
|
Range | Imprecise variant inner-bounding range | ||
|
component:outer-start-end
|
0..1 | Outer Start-End | ||
|
code
|
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]
|
Range | Imprecise variant outer-bounding range | ||
|
component:coordinate-system
|
0..1 | Coordinate System | ||
|
code
|
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.. | CodeableConcept |
0-based interval counting | 0-based character counting | 1-based character counting Binding: todo ( extensible ) |
|
|
component:ref-allele
|
0..1 | Genomic Ref Allele | ||
|
code
|
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]
|
string | Normalized string per the VCF format. | ||
|
component:alt-allele
|
0..1 | Genomic Alt Allele | ||
|
code
|
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]
|
string | Normalized string per the VCF format. | ||
|
component:coding-change-type
|
0..1 | Coding DNA Change Type | ||
|
code
|
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.. | 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 | Genomic Source Class | ||
|
code
|
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.. | CodeableConcept |
Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: todo ( extensible ) |
|
|
component:sample-allelic-frequency
|
0..1 | Sample Allelic Frequency | ||
|
code
|
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]
|
Quantity | Relative frequency in the sample | ||
|
system
|
Required Pattern: http://unitsofmeasure.org | |||
|
component:allelic-read-depth
|
0..1 | Allelic Read Depth | ||
|
code
|
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]
|
Quantity | Unfiltered count of supporting reads | ||
|
component:allelic-state
|
0..1 | Allelic State | ||
|
code
|
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.. | CodeableConcept |
Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: todo ( extensible ) |
|
|
component:variant-inheritance
|
0..1 | Origin of germline genetic variant | ||
|
code
|
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.. | CodeableConcept |
Maternal | Paternal | Unknown Binding: todo ( extensible ) |
|
|
component:variant-inheritance-basis
|
0..1 | Evidential basis for variant inheritance | ||
|
code
|
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.. | CodeableConcept |
Directly measured | Family DNA | Family history | Inferred from population data Binding: todo ( extensible ) |
|
|
component:variation-code
|
0..* |
Variation Code |
||
|
code
|
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.. | CodeableConcept |
ClinVar ID or similar Binding: todo ( example ): Multiple bindings acceptable |
|
|
component:chromosome-identifier
|
0..* |
Chromosome Identifier |
||
|
code
|
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.. | CodeableConcept |
Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: todo ( required ) |
|
|
component:representative-protein-hgvs
|
0..1 | Protein (Amino Acid) Change - pHGVS | ||
|
code
|
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.. | 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 | Genomic Structural Variant Copy Number | ||
|
code
|
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]
|
C | Quantity | cnt-3: There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. | |
|
component:variant-confidence-status
|
0..1 | Variant Confidence Status | ||
|
code
|
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.. | CodeableConcept |
High | Intermediate | Low Binding: Variant Confidence Status ( required ) |
|
|
component:repeat-motif
|
0..* |
Repeat Motif |
||
Slices for extension
|
Slice: Unordered, Open by value:url | |||
|
repeat-motif-order
|
0..1 | positiveInt |
Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order |
|
|
code
|
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.. | string | CAG | |
|
component:repeat-number
|
0..* |
Repeat Number |
||
|
Slices for extension
|
Slice: Unordered, Open by value:url | |||
|
repeat-motif-order
|
0..1 | positiveInt |
Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order |
|
|
code
|
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.. | Quantity | 40 | |
|
Documentation for this format
|
||||