Applying to university directly?

I have applied through UCAS and used all my five choices and received offers. I am an international applicant and according to the university I can apply directly for their foundation course, the foundation course leads to a totally different degree than my UCAS choices.
I emailed the university about my case, they replied that send your application directly to us, does this mean it won't affect my UCAS choices?
They did not directly mention anything about whether it will affect or no
I just want be sure before sending my application

If the uni are allowing you to do this, then it should be fine. Often unis will consider students for foundation courses if they aren't quite suitable for the course they originally applied for. Do they want you to just confirm you'd like to be considered for the course, or do they want more information?

I have the relevant A level subjects for the course which I applied to via UCAS , but for this "new" course I don't have the relevant subjects so I have to do foundation , and this univeristy isn't in my five ucas choices, so this is the sixth univeristy
No, they don't want more information.

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Ah, I see, so it's not a university you've applied to at all?

In theory, they should now only let you apply through extra- they shouldn't be letting you submit another application. In this case, I would clarify the situation with UCAS. If it's all done outside the UCAS system, your offer would have less legal standing if the uni wanted to get out of it at some stage (although they are supposed to honour all offers made in writing).