Space for church organ frequently left above (4)
I believe the answer is:
loft
'space for church organ' is the definition.
(as in an organ loft)
'frequently left above' is the wordplay.
'frequently' becomes 'oft' (oft can mean frequently, eg oft-quoted).
'left' becomes 'l' (common abbreviation).
'above' is a charade indicator (letters next to each other) (in a down clue, some letters go above others).
'oft' put after 'l' is 'LOFT'.
(Other definitions for loft that I've seen before include "Roof space area" , "Kick high in the air" , "Throw up; pigeon house" , "Room At The Top" , "Propel through the air" .)