Manual? Might be a your throwout bearing. One of the arms could have bent perhaps, or even broken off. I did that with my 97 Type R Integra...several times. Similar 'clanking' until I did a clutch/flywheel replacement and saw the bearing shot to hell. The bearing housing was in the place it should be, but not seated because of the broken arm and would rattle upon acceleration and engine braking.
Put the car in neutral, then slowly rev it all the way up. Then come down slow on the accelerator. Is the noise present?
Still in neutral, rev up quick, hold for 5 secs, then come off it fast. Any noise?
If yes, you might have a serious issue. If no, start looking under the carriage for rocks between rotor guards, worn cv's, then you might have to open the transmission and look at the bearing.
The honda trans had a bearing with two 'hook' arms. One broke off, and the noise was the only indication; no difficulty shifting, no 'grinding noise' etc.
Best of luck!
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