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.
I have tried the Intel® Processor Diagnostic Tool and the last step CPU stress test caused the same problem that I receive in-game yet the test said that I passed? Any other suggestions?
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.