This is a nonexistent worry. mATX has to fit full size GPUs to meet the spec. mITX can -sometimes- be an issue, but even then, the vast majority of even mITX cases fit full sized GPUs
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PCPartPicker part list:
http://pcpartpicker.com/p/Vd7qcf
Price breakdown by merchant:
http://pcpartpicker.com/p/Vd7qcf/by_merchant/
CPU: Intel Core i5-6500 3.2GHz Quad-Core Processor ($199.98 @ OutletPC)
Motherboard: Gigabyte GA-H110M-A Micro ATX LGA1151 Motherboard ($53.88 @ OutletPC)
Memory: Crucial 8GB (1 x 8GB) DDR4-2133 Memory ($36.99 @ Amazon)
Storage: Seagate 1TB 3.5" 7200RPM Hybrid Internal Hard Drive ($69.89 @ OutletPC)
Video Card: XFX Radeon R9 380 4GB Double Dissipation Video Card ($189.99 @ Newegg)
Case: Fractal Design Core 1000 USB 3.0 MicroATX Mid Tower Case ($34.99 @ Micro Center)
Power Supply: SeaSonic S12II 520W 80+ Bronze Certified ATX Power Supply ($55.99 @ SuperBiiz)
Total: $641.71
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2016-02-02 17:27 EST-0500
Much better CPU, much better GPU, Hybrid Drive, better PSU.