Update and sort the list of clinical significance values

[tskir]

Related to EBIvariation/CMAT#243.

When running the ClinVar pipeline, it was discovered that two levels of clinical significance values are present in ClinVar, but not in our schema. This discrepancy has been present for a while, it just didn't trigger before because less evidence strings were generated (only the EFO mapped ones).

I've added the two missing levels (“confers sensitivity” and “conflicting data from submitters”) and also sorted the list lexicographically for readability.

[ireneisdoomed]

@DSuveges How would we go about this regarding the scoring? We would need to assign these clinical significances to a category to adjust the weight, right? Also to update the ETL config file and our documentation.

[DSuveges]

@ireneisdoomed

We would need to assign these clinical significances to a category to adjust the weight, right? Also to update the ETL config file and our documentation.

Yes, that's correct. So we have two new categories:

 "confers sensitivity",
"conflicting data from submitters",

There are 5 tiers in the score map: 0, 0.3, 0.5, 0.7, 0.9. I think confers sensitivity rather matches 0.5, while conflicting data from submitters matches 0.3.

[ireneisdoomed]

All good.