Among many other things, like the Clone Saga clones having his powers, a Sentinel straight up scans Peter Parker and mistakes him for a mutant because his DNA has literal spider genes in it now. That's just Spidey canon.

Same with Super-soldier Serum that gave Rogers his power, it was a genetic modification and, eventually, the same is true of Weapon VI aka Luke Cage (Weapons Plus being a descendant program, he received a modified version of the Serum)

In Marvel comics there's generally a distinction between "mutants" and "mutates." A mutant got their powers from birth, typically from the X-gene, a mutate had something happen to them, but that's not a real scientific distinction. They've all been mutated. It's just in-universe discrimination and is often specifically portrayed as such. Like all discrimination, the distinction is quite often arbitrary and unjustified.

They've been occasionally been referred to as “mutates”, as opposite to “natural” x-gene carrying mutants.

Also if their powers (or some form of power) can be inherited by their children (or clones), there's probably been some genetic change.

This is definitely the case for Spider-Man (so many clones! 😩) or the Hulk (though that could be radiation poisoning), and might be the case for the Fantastic Four (though it depends on the writer, and one of their children is a mutant, not a mutate, and radiation poisoning is also a possibility in their case).