Subtle difference pest is leaving (6)
I believe the answer is:
nuance
'subtle difference' is the definition.
(I've seen this in another clue)
'pest is leaving' is the wordplay.
'pest' becomes 'nuisance' (both can mean an annoying person).
'leaving' indicates named letters should be taken away.
'nuisance' with 'is' removed is 'NUANCE'.
(Other definitions for nuance that I've seen before include "Delicate shade of meaning" , "Subtlety, nicety" , "Delicate shade of difference" , "A slight shade or trace" , "Subtle shade of meaning" .)