| Name | Flags | Card. | Type |
Description & Constraints
|
|---|---|---|---|---|
Observation
|
GenomicImplication | Molecular Consequence | ||
code
|
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 |
|
component: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: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: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:feature-consequence
|
0..* |
Feature Consequence |
||
|
code
|
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.. | CodeableConcept |
stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence ( extensible ): Concepts in sequence ontology under SO:0001537. |
|
|
component:functional-effect
|
0..1 | Functional Effect | ||
|
code
|
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.. | CodeableConcept |
gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more) Binding: Functional Effect ( extensible ): Sequence Ontology terms under SO:0001536 |
|
|
Documentation for this format
|
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