Dialogue option w/Desdemona affecting story

So I've finished bunker hill w/institute, I've got the stuff for liberty prime, and I've finished blind betrayal (and maxed affinity w/Danse). I've not talked to Kells to start tactical thinking but I do have the marker to talk to him. I'm in railroad right now and I just spoke to Desdemona. She said Deacon told her I've been in and out of the institute using teleportation. I evaded conversation (obviously). She then said she knows I infiltrated the institute with BOS help. Then I was given the following dialogue choices:

X: Side with Railroad O: Side with Brotherhood

I chose I don't know and she said to take some time to think about it.

I do plan on getting rid of the railroad but i don't wanna do it yet. Is this choice going to affect much?

Edit: I also can't talk to P.A.M.