This issue has arisen recently and has annoyed the hell out of me. Unfortunately I can't pinpoint a potential culprit, but I have a slight idea as to what it could be.
My first suspect is the PSU. It's an A-tier PSU (MSI A650GF) and I got it for the value of the price, but it's not out of the question. Particularly since the sound gets really quiet either on its own or when I make vibrations on the floor (i.e. stomping).
I have considered replacing it with a Seasonic PX-650, in case the PSU is the culprit in this case. Feedback on this matter would be greatly appreciated.