coordinate system and HGVS usage

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    • Type: Change Request
    • Resolution: Persuasive with Modification
    • Priority: Medium
    • Genomics Reporting (FHIR)
    • STU3
    • Clinical Genomics
    • STU
    • (profiles) [deprecated]
    • 2.16.2
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      put text in doc on this and explore invariant fhir path option

      add Larry's comment "HGVS is 1-based positional with special rules for consideration that can be less than straight forward when switching between insertions and deletions"

      Show
      put text in doc on this and explore invariant fhir path option add Larry's comment "HGVS is 1-based positional with special rules for consideration that can be less than straight forward when switching between insertions and deletions"
    • Clem / Patrick : 17-0-1
    • Clarification
    • Non-substantive

      the SD for Described Variant (Discrete or Structural) has components for using HGVS while in other components allows the user to enter coordinate systems and genomic references, etc.

      HGVS is by definition 1-based (their version of it). There needs to be guidance to say if HGVS is used, the rest of the instance should also be 1-based and not to mix coordinate systems in a resource instance.

            Assignee:
            Unassigned
            Reporter:
            Bob Milius
            Watchers:
            1 Start watching this issue

              Created:
              Updated:
              Resolved: