Fix #5017 - ClinVar classifications of pathogenicity

[dnil]

This PR adds a functionality or fixes a bug.

• Fix #5017

Testing on cg-vm1 server (Clinical Genomics Stockholm)

**Prepare for testing** 1. Make sure the PR is pushed and available on [Docker Hub](https://hub.docker.com/repository/docker/clinicalgenomics/scout-server-stage) 1. Fist book your testing time using the Pax software available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). The resource you are going to call dibs on is `scout-stage` and the server is `cg-vm1`. 1. `ssh @cg-vm1.scilifelab.se` 1. `sudo -iu hiseq.clinical` 1. `ssh localhost` 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps` 1. Stop the service with current deployed branch: `systemctl --user stop scout.target` 1. Start the scout service with the branch to test: `systemctl --user start scout@` 1. Make sure the branch is deployed: `systemctl --user status scout.target` 1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](https://pax.scilifelab.se), which will release the allocated resource (`scout-stage`) to be used for testing by other users.

Testing on hasta server (Clinical Genomics Stockholm)

**Prepare for testing** 1. `ssh @hasta.scilifelab.se` 1. Book your testing time using the Pax software. `us; paxa -u -s hasta -r scout-stage`. You can also use the WSGI Pax app available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `conda activate S_scout; pip freeze | grep scout-browser` 1. Deploy the branch to test: `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b ` 1. Make sure the branch is deployed: `us; scout --version` 1. After testing is done, repeat the `paxa` procedure, which will release the allocated resource (`scout-stage`) to be used for testing by other users.

How to test:

1. how to test it, possibly with real cases/data

Expected outcome: The functionality should be working Take a screenshot and attach or copy/paste the output.

Review:

• [ ] code approved by
• [ ] tests executed by

[sonarcloud[bot]]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[dnil]

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.76%. Comparing base (1a81fe4) to head (4549e02). Report is 1 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #5020 +/- ## ======================================= Coverage 84.76% 84.76% ======================================= Files 320 320 Lines 19353 19353 ======================================= Hits 16405 16405 Misses 2948 2948 ```

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[dnil]

Mm, I think this is more or less ok with this, and then we can improve a bit further when we start getting CLNSIGCONF parsed in from the pipelines.

I worry about the conflicting variants not being up there with a clinical filter grade REVSTAT, but running the numbers make me feel a little better: The number of conflict status vars with a P/LP classification in the mix is larger than one would desire (17k) but compared to the total of 1.1M variants it's not a huge issue. I'm sure this will bite on a case here and there, but for the bulk it means less needless clicks over to clinvar.

EDIT: latest ClinVar ref dump numbers

[dnil]

https://github.com/Clinical-Genomics/scout/blob/02b3dc50bb37c47aef97daba46d7958f27ce73f7/scout/build/variant/clnsig.py#L18 The loading logs must be rather crowded. I do so wish we had a regular log audit, or at least someone from prod to notify us when something happens in the warnings/errors department. There is something to crashing early.. 😁