Noise is heard while moving from one gear to another gear.
Car Problem Diagnosis
While shifting from two or more gears when a noise is heard it’s an indication of a problem inside the manual transmission that rotates every time. Since this problems is cause by a rotating parts inside the transmission, the possible cause of the problem is the main shaft bearings and the input shaft bearings because this parts always rotates at all speed, however this is only a possibility, there may be other problems which can only be detected with actual inspection of the transmission, it should be opened to analyze better by a professional.
Possible Cause of Transmission Problem.
Problem with main shaft bearing or input shaft bearings
All About Auto Advice
No other option but to bring your car to a service center that specialized in manual transmission, the transmission is needed to be opened up for better examination of the cause of the problems, you are lucky if the car is still under warranty because this will cover all the cost incurred during repair, however if the car is beyond warranty, better bring your car to a reputable auto repair shop that does this kind of job.