Details
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Change Request
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Resolution: Persuasive
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Medium
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Genomics Reporting (FHIR)
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1.0 [deprecated]
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Clinical Genomics
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(profiles) [deprecated]
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James Jones / Kevin Power: 9-0-0
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Correction
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Compatible, substantive
Description
Propose to remove the following components from the Variant profile:
Field | Reason |
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component:dbSNP-id | Combine into 'variation-code' component (see below) |
component:variant-length | Unused, no known use case |
component:chromosome-copy-number-change-type | Unused, no know use case |
component:arrCGH-ratio | Unused, no known use case |
component:complex-var-type | Could look to integrate with Haplotype? |
Regarding dbSNP
Recognizing the history of why we had a separate component, wanted to comment on this suggestion in more detail. This change should also come with additional guidance on the 'variation-code' component which generically describes the usage as a code that is simply a reference to a variant knowledge source. This guidance should indicate that it is well understood that many variant knowledge sources have limitations and varying levels of detail, using dbSNP as an example that is really more a 'location' that a 'variant' to help illustrate the point. To help illustrate the difference with dbSNP, we should add an invariant that would enforce that if a dbSNP is included in the 'variation-code' component, the 'alt-allele' component should be required.