cancervariants / cancervariants/variation-normalization

Frameshift variants should not return valid VRS objects in gnomad_vcf_to_protein

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#652 1 comment 0 reactions 0 assignees View on GitHub
bug
Dominant language
Python
Stars
15
Forks
2
PR merge metrics
No merged PRs in 30d

Description

### Describe the bug

VRS does not currently support variants where there is a resulting frameshift. We should detect this and return an error. Currently, we return incorrect VRS objects in cases of frameshifts

### Steps to reproduce

1. Attempt to normalize vcf coords that are known to result in a frameshift in the /gnomad_vcf_to_protein endpoint (ex: 17-43124028-CTCT-CT)
2. notice that there is a VRS object returned

### Expected behavior

We should not return a VRS Allele since VRS does not support fs variants currently. We should return a warning saying "Frameshift variants are currently not supported" or something of that sort

### Current behavior

valid vrs allele returned

### Possible reason(s)

we don't check for it

### Suggested fix

check for if a variant results in a frameshift before converting/returning

### Branch, commit, and/or version

any

### Screenshots

_No response_

### Environment details

Not applicable

### Additional details

:)

### Contribution

None

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the /gnomad_vcf_to_protein request with 17-43124028-CTCT-CT and trace the endpoint's variant conversion path. Confirm that frameshift results produce a warning such as "Frameshift variants are currently not supported" and no VRS Allele, then run the relevant endpoint tests if available.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api, bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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