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Clinvar variant data does not contain "1" for likely pathogenic. #247

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holtgrewe opened this issue Oct 16, 2023 · 1 comment · Fixed by #258
Closed

Clinvar variant data does not contain "1" for likely pathogenic. #247

holtgrewe opened this issue Oct 16, 2023 · 1 comment · Fixed by #258
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bug Something isn't working

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@holtgrewe
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Describe the bug
Looking at the output of BRCA1 variants, no "likely pathogenic" variants are written out.

Reproduce

# curl '[https://reev.cubi.bihealth.org/internal/proxy/annonars/genes/clinvar?hgnc_id=HGNC:1100'](https://reev.cubi.bihealth.org/internal/proxy/annonars/genes/clinvar?hgnc_id=HGNC:1100%27) -H 'User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:109.0) Gecko/20100101 Firefox/117.0' -H 'Accept: */*' -H 'Accept-Language: en-US,en;q=0.5' -H 'Accept-Encoding: g
zip, deflate, br' -H 'Referer: [https://reev.cubi.bihealth.org/gene/HGNC:1100/grch37'](https://reev.cubi.bihealth.org/gene/HGNC:1100/grch37%27) -H 'Connection: keep-alive' -H 'Sec-Fetch-Dest: empty' -H 'Sec-Fetch-Mode: cors' -H 'Sec-Fetch-Site: same-origin' -H 'TE: trailers' > /tmp/data.json
# jq .genes[].variants[].variants[].clinsig /tmp/data.json | sort | uniq -c
 12974 0
 12540 2
 11328 3
  2614 4
@holtgrewe holtgrewe added the bug Something isn't working label Oct 16, 2023
@holtgrewe
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I double-checked now the current annonars code, and it appears that everything should work fine. I'll create a PR to make things more robust. Maybe we just need to rebuild the database with the latest code.

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