Quick Google- height of 3.58” (91 mm), width of 12.6” (320 mm), depth of 10.2” (259.1 mm)
Looks tight, a very low profile cpu cooler would be needed.
I was thinking a side by side layout might work better, but you then have trouble finding space for the psu.
One option that could work is somewhere between the two, io to one side, gpu partially above the board, fans facing up.
That would give you more height for the cpu cooler and avoid having to intake both top and bottom, but the io on the side won't look great.
I am pretty sure people have put itx systems in old xbox cases, try searching for that to see what others have manages already.