It is the input shaft bearing, It did that on my Honda with no ill affect till it caused so much play in my input shaft that it caused my rear main to begin to leak and ruin my clutch.
Then I just drove it with a slipping clutch for 2k miles, even took it on a 300 mile trip with a rear main leak and oily clutch, by the end of the 2k the input shaft bearing itself fell apart, and then the noise got REALLY loud, and occasionally one of the loose bearings in the transmission would slide into a cog and make an interesting grinding noise randomly while driving, I drove it until the next weekend because I couldn't tear down mid week. I installed a new transmission, rear main, clutch kit and flywheel, its g2g now.
Hopefully your transmission input shaft noise doesn't go as south as mine... because if you do not know how to fix it by yourself, you can be out a lot of $$ for the repairs.