minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions
{
"resourceType" : "Observation",
"id" : "gx-genomic-variant-somatic-bap1-indel",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant"
]
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"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation gx-genomic-variant-somatic-bap1-indel</b></p><a name=\"gx-genomic-variant-somatic-bap1-indel\"> </a><a name=\"hcgx-genomic-variant-somatic-bap1-indel\"> </a><a name=\"gx-genomic-variant-somatic-bap1-indel-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-gx-cancer-patient-adam-anyperson.html\">Adam Anyperson Male, DoB: 1990-01-01 ( Medical Record Number: 123456789)</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Practitioner-us-core-practitioner-owen-oncologist.html\">Practitioner Owen Oncologist </a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:950}, {https://www.ncbi.nlm.nih.gov/gene 3815}\">BAP1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004656}\">NM_004656.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_004656.4:c.1768C>T}\">NM_004656.4:c.1768C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_004647.1:p.(Gln590Ter)}\">NP_004647.1:p.(Gln590Ter)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 57.4 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code% = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org/ SO:0001587}\">stop_gained</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote></div>"
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"code" : {
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"code" : "69548-6"
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"subject" : {
🔗 "reference" : "Patient/gx-cancer-patient-adam-anyperson"
},
"effectiveDateTime" : "2019-04-01",
"performer" : [
{
🔗 "reference" : "Practitioner/us-core-practitioner-owen-oncologist"
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"display" : "Present"
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