140mm fans need 35mm clearance

120mm fans need 30mm clearance

92mm fans need 23mm clearance

So in previous iterations of this design I've put the GPU in front (that is, on the left side of the case) of the motherboard, but I want to explain a bit why I settled on having it behind instead.First off, I have to stress the importance of intake clearance for fans. Too little will reduce airflow considerably, and both cooling performance and noise will be adversely affected. Cases like the Phanteks Evolv ITX don't leave enough room between the GPU intake and the PSU shroud, and temperatures suffer for it.What's an appropriate amount of clearance, then? Well, admittedly I haven't experimentally tested this, but what I've settled on as a "probably good enough" rule of thumb is one quarter of the fan diameter of clearance. This is based on calculating the area the air must flow through - namely the disc of the fan, and the area of an imaginary cylinder forming the boundary of the intake area - and making them about equal. See this image for an explanation:For example:Note I use 0.25 of the fan diameter only as a general target to aim for,as an absolute rule. More is probably better, but a bit less will suffice as well.So for this style of layout, where the GPU and motherboard are sandwiched together, putting the GPU behind the motherboard actually makes better use of space than the reverse. That's partly because we have a large area where the GPU extends past the motherboard, but also because we can use the space that's required, but otherwise unused, for the motherboards standoffs/backside clearance:As is plainly apparent, the layout on the right provides considerably more intake clearance for the GPU fans. Now, depending on what drives are mounted or whether we end up putting in an SFX PSU, that area towards the front may be considerably reduced, but it's still going to be better than with the GPU facing the side of the case.A secondary reason why I believe the GPU-behind-the-motherboard layout is superior is because it better isolates the GPU from the front side of the motherboard, where the GPU exhaust could enter the CPU cooler:There are some other benefits as well having to do with fitment rather than airflow. Tubing to the bottom rad, for example, is likely to be easier to run with the GPU pushed all the way to the right side of the case. Also, in the case where a full custom loop is installed and a full cover, single slot block on the GPU, the space opened up behind the motherboard could be used for SSD mounting.Structurally, there's some advantage to having the motherboard tray in the center of the case, as it would be attached to the top beam (which must support the full weight of the case with a handle attached).