It's generally only connected to the motherboard for power, the lines that control speed go to the knob. There might be some way to modify it if you're good with electronics, but otherwise you just have to adjust it yourself. I have the same thing with my Scythe Setsugens, although I plugged their power end into a fan controller instead of the mobo so I can adjust all my cooling fans from the front of my case.
But anyway the only way for it to be controlled VIA afterburner would be if the power wires plug into the card at the same spot the default cooler did, with the same wires and everything. Again, possibly can be done with a mod.