FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting |
| Resource Type | Parameters |
| Id | Parameters-FindSubjectMolecConseqOutput.json |
| FHIR Version | R4 |
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FHIR
FHIRsmith{
"resourceType": "Parameters",
"id": "FindSubjectMolecConseqOutput",
"parameter": [
{
"name": "consequence",
"resource": {
"resourceType": "Observation",
"id": "MC1",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001395525.1:c.-281+2T>C - intronic_variant:loss_of_function_variant</div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "molecular-consequence"
}
]
},
"subject": {
"reference": "Patient/HG00403"
},
"effectiveDateTime": "2023-04-01",
"performer": [
{
"reference": "Organization/ExampleOrg"
}
],
"interpretation": [
{
"coding": [
{
"system": "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
"code": "HIGH",
"display": "High"
}
]
}
],
"derivedFrom": [
{
"reference": "Observation/variantExampleMC"
}
],
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7",
"display": "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_001395525.1",
"display": "NM_001395525.1"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "feature-consequence"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001575",
"display": "splice_donor_variant"
},
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001627",
"display": "intron_variant"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "functional-effect"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO_0002054",
"display": "loss_of_function_variant"
}
]
}
}
]
}
},
{
"name": "consequence",
"resource": {
"resourceType": "Observation",
"id": "MC2",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001366781.1:c.90T>C - synonymous_variant</div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "molecular-consequence"
}
]
},
"subject": {
"reference": "Patient/HG00403"
},
"effectiveDateTime": "2023-04-01",
"performer": [
{
"reference": "Organization/ExampleOrg"
}
],
"interpretation": [
{
"coding": [
{
"system": "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
"code": "LOW",
"display": "Low"
}
]
}
],
"derivedFrom": [
{
"reference": "Observation/variantExampleMC"
}
],
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6"
}
],
"text": "coding HGVS"
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_001366781.1:c.90T>C",
"display": "NM_001366781.1:c.90T>C"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7",
"display": "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_001366781.1",
"display": "NM_001366781.1"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "feature-consequence"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001819",
"display": "synonymous_variant"
}
]
}
}
]
}
},
{
"name": "consequence",
"resource": {
"resourceType": "Observation",
"id": "MC3",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "molecular-consequence"
}
]
},
"subject": {
"reference": "Patient/HG00403"
},
"effectiveDateTime": "2023-04-01",
"performer": [
{
"reference": "Organization/ExampleOrg"
}
],
"interpretation": [
{
"coding": [
{
"system": "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
"code": "MOD",
"display": "Modifier"
}
]
}
],
"derivedFrom": [
{
"reference": "Observation/variantExampleMC"
}
],
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6"
}
],
"text": "coding HGVS"
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_001395543.1:c.-171T>C",
"display": "NM_001395543.1:c.-171T>C"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7",
"display": "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
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{
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"code": "NM_001395543.1",
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}
]
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "feature-consequence"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001623",
"display": "5_prime_UTR_variant"
}
]
}
}
]
}
},
{
"name": "consequence",
"resource": {
"resourceType": "Observation",
"id": "MC4",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "molecular-consequence"
}
]
},
"subject": {
"reference": "Patient/HG00403"
},
"effectiveDateTime": "2023-04-01",
"performer": [
{
"reference": "Organization/ExampleOrg"
}
],
"interpretation": [
{
"coding": [
{
"system": "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
"code": "MOD",
"display": "Modifier"
}
]
}
],
"derivedFrom": [
{
"reference": "Observation/variantExampleMC"
}
],
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7",
"display": "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
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{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_001395544.1",
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}
]
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "feature-consequence"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001627",
"display": "intron_variant"
}
]
}
}
]
}
},
{
"name": "variant",
"resource": {
"resourceType": "Observation",
"id": "variantExampleMC",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Variant</div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69548-6",
"display": "Genetic variant assessment"
}
]
},
"subject": {
"reference": "Patient/HG00403"
},
"effectiveDateTime": "2023-04-01",
"performer": [
{
"reference": "Organization/ExampleOrg"
}
],
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "Present"
}
]
},
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48002-0",
"display": "Genomic source class"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6683-2",
"display": "Germline"
}
]
}
},
{
"code": {
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{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence ID"
}
]
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"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NC_000001.10"
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{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "53034-5",
"display": "Allelic state"
}
]
},
"valueCodeableConcept": {
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{
"system": "http://loinc.org",
"code": "LA6706-1",
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{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81252-9",
"display": "Discrete genetic variant"
}
]
},
"valueCodeableConcept": {
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{
"system": "http://varnomen.hgvs.org",
"code": "NC_000001.10:g.86852621A>G",
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}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81258-6",
"display": "Sample VAF"
}
]
},
"valueQuantity": {
"value": 0.6,
"unit": "relative frequency of a particular allele in the specimen",
"system": "http://unitsofmeasure.org",
"code": "1"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69547-8",
"display": "Genomic Ref allele [ID]"
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]
},
"valueString": "A"
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{
"code": {
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"system": "http://loinc.org",
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]
},
"valueString": "G"
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{
"code": {
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"system": "http://loinc.org",
"code": "92822-6",
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"valueCodeableConcept": {
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{
"system": "http://loinc.org",
"code": "LA30100-4",
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},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81254-5",
"display": "Genomic allele start-end"
}
]
},
"valueRange": {
"low": {
"value": 86852620
}
}
}
]
}
}
]
}