We at least have a consensus on what "eye color" is.
Nobody really has a clue what "intelligence" is. In terms of anatomy and physiology.
It's like asking; What are the genes responsible for consciousness?
Even more complicated since "intelligence" is an aspect of both consciousness and subconscious processes.
Your objection was that we don't know exactly how the SNPs cause the intelligence, and maybe now you see how the objection fails. Regardless of what we don't know about intelligence, we still know a helluva lot about it. Intelligence is something we can observe, measure, quantify, we know the variations are heritable, and we can identify some of the SNPs that code for those variants. Before the discovery of DNA, genetics was likewise largely an abstraction. We had only indirect evidence for the existence of genes. That was no good reason to say, "Therefore, the theory of evolution is bullshit." That's what you would do if your politics asked for it. Your objections are not motivated by an attempt to make sense of the science. But, anti-scientific politics does the politics no good. Liberalism will be hurt most of all by such willful blindness.