Frameshift variants should not return valid VRS objects in gnomad_vcf_to_protein

[katie-perry]

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

[korikuzma]

Adding AC for the ticket.

Current test:

resp = await test_handler.gnomad_vcf_to_protein("17-43124028-CTCT-CT")
    # No assertion checks since this should not return a VRS object (frameshifts are not supported in VRS)
    assert resp.gene_context
    assert resp.warnings == []

Should be changed to:

resp = await test_handler.gnomad_vcf_to_protein("17-43124028-CTCT-CT")
    # No assertion checks since this should not return a VRS object (frameshifts are not supported in VRS)
    assert not resp.variation  # <- Add this line
    assert resp.gene_context
    assert resp.warnings == []