'Cause the engine's vibration frequency changes.

    There are several things that are different when the clutch is
depressed. If everything is working correctly, when you press down the
clutch the shaft into the transmission and the clutch disk should stop
turning and the throw-out bearing should be turning (with the clutch out
the throw-out bearing should stop and the tranny shaft and clutch should
turn). That change might cause something innocent that is rattling to
stop rattling. But that could be a sign of something not quite right
with your transmission or clutch if it is causing a vibration that is
showing up elsewhere. Or the sound could be coming directly from one of
those components (throw-out bearing clutch or tranny shaft). Or it could
be that just the change in mass of rotating parts changes the frequency
enough to make the rattle disappear.
    No one is going to be able to tell you what the noise is without more
info. Are you having any problems with the shifting? When you press the
clutch just lightly what happens to the sound? More than likely it is
going to take someone observing directly at the parts with the car
running to find where it is coming from.

-jim

-jim

I have seen only a couple of bad throw out bearing and they made noise when the clutch peddle was depressed, not when the clutch was engaged.