On my 2001 Toyota Corolla 4AFE engine, on iddle the transmission make a ratling sound like there's something vibrating. My dad says it's probably a bearing or loose flywheel.
Here's is a short video.
https://www.youtube.com/watch?v=DOK8xQoSEqc
However it's sliced and diced, it's not good. Gear teeth could be going bad. Cluster gear assembly may be disassembling. It could be the shaft gears.
Or, it could be a shaft bearing, as your father says. The cheapest and most benign thing it could be is a loose transmission mount. If and when the car is on a lift, that could easily be ruled in or out. But to drive it with a loose mount will create damage, if that is what it is.
The probabilities are that the internals are damaged, though. Bad news, I know.
Oh that's sad. I hope it is not something that bad. Something worth mentioning is that the sound don't change when the clutch is in or out. And it sounds like that only on iddle, also the 1st gear has a whiny noise like it would be reverse gear
The whining noise is most likely the clutch/flywheel, as your father says.
Manual or automatic transmission?
It's Manual