2002 Honda Civic manual transmission rattling noise in 1st and 2nd gears?

It sounds like putting a playing card in a turning bicycle wheel, or sticking a paper in a low speed fan. It's very loud in 1st, a bit lower in 2nd and I barely hear it in the 3rd gear. 4 and 5 are fine. The frequency of the noise increases with rpm. When the clutch is disengaged, the noise goes away. The shift stick doesn't have any vibration and I can shift fine. The car has cold air intake. The sound comes and goes, but it's usually heard.