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Differing transcript versions in WebApp and API-calls #2171

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KuechlerO opened this issue Dec 28, 2024 · 0 comments
Open

Differing transcript versions in WebApp and API-calls #2171

KuechlerO opened this issue Dec 28, 2024 · 0 comments
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@KuechlerO
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Differing transcript versions between Varfish API endpoints and frontend
Hi, I have stumbled on some cases, where the displayed transcript versions in the frontend under VarFish Variant Details differs to the annoted transcript version given by the API endpoint.
Depending on which specific transcript and version is regarded, this might lead to alternative HGVS annotations.

To Reproduce
I'm not sure, whether it's fine to share VarFish-UUIDs here.
If yes, then I can add my project and variant IDs.

Steps to reproduce the behavior:

  1. Call Frontend and go to a Case --> Variant Annotation --> Variant Detail View
    --> Check transcript ID and version under Consequences
  2. Call API - user-annotated-case:
    https://varfish.bihealth.org/variants/ajax/smallvariant/user-annotated-case/<ID>
    --> Check transcript ID and version

Transcript versions can differ. For me the following points are not clear:

  • If multiple transcripts are displayed, which transcript is returned with the API call? As far as I can see it does not have to be the MANE transcript
  • Which transcript version is returned? My guess is, that the version that has been used at the time of user annotation is returned?!

Finally, do I understand correctly that the Variant consequences displayed in the WebApp are stemming from the Mehari-Call?
Thus, these results are available with this endpoint:
"https://varfish.bihealth.org/proxy/varfish/mehari/seqvars/csq?<params>"
Are these results constantly updated? (So that always the most up-to-date transcript version is displayed?)

Expected behavior
I expected the output for the call API - user-annotated-case to agree with the WebApp output.

Additional context
This issue is related to Max' issue: #863

Btw
The URL for Varfish discussions seems to be broken:
https://github.com/varfish-org/varfish-server/discussions

@KuechlerO KuechlerO added the bug Something isn't working label Dec 28, 2024
@KuechlerO KuechlerO changed the title Differing transcript versions Differing transcript versions in WebApp and API-calls Dec 28, 2024
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