LoF annotation in OmicsSomaticMutations.csv

In the documentation for the new mutation file, it states that the LoF column should be Y if “loss of function according to revel (score >.9) or a set of validated BRCA1 locations”.

However, only the latter appears to be true. There are no non-BRCA1 variants with an LoF=Y.

Even variants like TP53 p.G244D which has a revel score of 0.953 and a Dann score of 0.998 are listed as LoF = NA.

What is the appropriate interpretation for the LoF column?


Thanks for pointing this out. You are correct - the LoF column currently only marks variants that scores <= -1.328 in the BRCA1 functional assay.

I also wanted to note that we are currently working on improving our mutation annotation and the definition might change in the future.