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  1. FHIR Specification Feedback
  2. FHIR-27748

Rename "Functional Annotation" Component to "Variant Consequence"

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    Details

    • Type: Change Request
    • Status: Applied (View Workflow)
    • Priority: Medium
    • Resolution: Persuasive with Modification
    • Specification:
      Genomics Reporting (FHIR)
    • Raised in Version:
      1.0
    • Work Group:
      Clinical Genomics
    • Related Page(s):
      genomics
    • Resolution Description:
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      • Rename the current 'functional-annotation' component to 'molecular-consequence'
      • Provide updated definition of Molecular Consequence
        • Changes in a structural features of a sequence due to the observed variant
      • Request a new LOINC code for Molecular Consequence
        • Update current TBD code from functional-annotation -> molecular-consequence
      • Binding on the current component remains the same (SO:0001537)
      Show
      Rename the current 'functional-annotation' component to 'molecular-consequence' Provide updated definition of Molecular Consequence Changes in a structural features of a sequence due to the observed variant Request a new LOINC code for Molecular Consequence Update current TBD code from functional-annotation -> molecular-consequence Binding on the current component remains the same (SO:0001537)
    • Resolution Vote:
      Arthur Herman/Rachel Kutner: 14-0-1
    • Change Category:
      Enhancement
    • Change Impact:
      Non-compatible

      Description

      The concept of "Functional Annotation" in the FHIR spec is tied to the Sequence Ontology list labeled "Structural_Variant" (http://sequenceontology.org/browser/current_svn/term/SO:0001537) which can be easily confused with the concept of Functional Effect. This list of terms seems to better correspond with what ClinVar refers to as the "Variant  Consequence", and would be less confusing if it were renamed as such to avoid confusion with "Functional Effect". 

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              Assignee:
              cerkyp Kevin Power
              Reporter:
              rkutner Rachel Kutner
              Watchers:
              4 Start watching this issue

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                Updated:
                Resolved:
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