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?