Humming Sound on Transmission

[Uno]

I am hearing a humming sound from the transmission of our Vios (Yaris Sedan) whenever I am engine braking on 1st, 2nd and 3rd Gears. I barely hear the sound on 4th and 5th maybe because of the roadnoise. Factory guys says it is just normal but the sound is to loud, comparing to other Vios I had rode.

My car is 55K Kilometers in odo, and well maintained by the Factory. My Service Advisor said it could be a release bearing, but, the sound occurs when I am on gear, trailing (engine braking) and the sound is gone when I press the clutch. They already lubed up some linkage and I believe one of it is the fork, but the sound was still there.

Any advice or idea what is this?