An afterthought, note, in church (4)
I believe the answer is:
apse
'in church' is the definition.
(I've seen this before)
'an afterthought note' is the wordplay.
'an' becomes 'a'.
'afterthought' becomes 'ps' (as in a PS in a letter).
'note' becomes 'e' (musical note).
'a'+'ps'+'e'='APSE'
(Other definitions for apse that I've seen before include "part of cathedral" , "Semicircular end of a church, behind the altar" , "Primate holds saint to be a" , "Where you could find a magistrate's chair" , "where praetor sat" .)