Stomach perhaps that makes a noise in church? (5)
I believe the answer is:
organ
'stomach perhaps' is the definition.
(stomach is a kind of organ)
'a noise in church?' is the wordplay.
I cannot really understand how this works, but
'a' could be 'an' and 'an' is located in the answer.
This may be the basis of clue (or it may be nonsense).
'that makes' acts as a link.
Can you help me to learn more?
(Other definitions for organ that I've seen before include "Functional unit of the body and musical instrument" , "Wind and keyboard instrument" , "Soft part of the body which has a specific function" , "Church keyboard instrument" , "Body part - wind instrument" .)