My dealership changed my pilot bearing and throw out bearing, because I was having some gear type of noise when I would tap on the gas around the 1-1,500rpms don't know if it's normal on the manuals since I've never owned one( this is my first manual). Sometimes I would hear it at idle and when it does it it vibrates the car a little. It didn't fixed my issue so I have to wait till they get another same model same mileage so they can test it and know if it's normal on my car. To answer your question, if your car is making some kind of grinding noise and it's dissapears when you press on he clutch that's the problem when those goes bad.
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