Not entirely silent upset stomach (3)
I believe the answer is:
tum
'stomach' is the definition.
(synonyms)
'not entirely silent upset' is the wordplay.
'not entirely' means to remove the last letter (not all of the word).
'silent' becomes 'mute' (synonyms).
'upset' says the letters should be written backwards.
'mute' with its last letter taken away is 'mut'.
'mut' reversed gives 'TUM'.
(Other definitions for tum that I've seen before include "Belly" , "Middle" , "Stomach (informal)" , "Corporation" .)