Here I have some recommendations for this situation.
First, when a GPU or video card is added to a system, the graphics from the processor would be disabled.
Now, regarding the issue, my recommendation would be to update to the latest driver from your GPU.
Secondly, I recommend you to run the Intel® Processor Diagnostic Tool to see if any issues are present in your Intel® Core™ i5-4690K Processor.
Thirdly, the other way to go would be to contact the manufacturer of your GPU to see if they are aware of the situation, since this is a recently released game, some issues may be present until updates or patches are released.
If any additional questions are present, do not hesitate to advise me.
Thank you for your reply.
Since after running the Intel® Processor Diagnostic Tool all the tests passed, my recommendation would be to contact your GPU manufacturer support to get more information or fixes for this situation.
I was able to find out that some other customers are having this issue, even with a very high end system, this may be related to the optimization performed by the developer of the game.
Here you can find some more information from forums for this situation: https://www.reddit.com/r/nvidia/comments/3ssvnp/low_fps_in_cities_fallout_4_gtx_970/
GPU/Game recommendations: GeForce GTX 970: NVIDIA's Recommended GPU For Fallout 4 | GeForce
Manufacturer of GPU support: Support | GeForce
Finally, if you encounter with any additional questions, do not hesitate to advise me.