Skin colour almost certainly doesn't affect intelligence (much). There are plenty of dark skinned upper caste Indians who are intelligent, for example.

We can predict skin colour reasonably well on the basis of very few genes. We need many more to predict intelligence (and we can't predict it nearly as well).

On the other hand, however...

...there are a lot of people who happen to have whatever genes cause dark skin who also happen to have lot of other genes that do other things...

Some of those others things include a genetic protection against malaria. Others confer a genetic protection against a nasty parasitic worm that prefers to live in the kidneys. The downside is that that protection itself is a bit unhealthy for the kidneys.

And some of them do a might good job of seeming like they cause lower intelligence. If we use our genetic prediction models, then they do in fact predict a lower intelligence.