Clarifying the headline: Every mutation of a single nucleotide of the human genome that could exist likely does in the human population. Just statistically this is very likely if not certain.

His second line of “but all the beneficial ones haven’t had time to become ubiquitous” reveals a weird misunderstanding of how evolution works. Not all beneficial mutations would necessarily ever become “ubiquitous”. And few if any mutations, especially on the scale of a single nucleotide, could fairly be characterized as objectively and universally “beneficial”. Environment and context is crucial.

Take the example of sickle cell disease, which can be caused by a single nucleotide mutation. It can cause many problems in its sufferers but it can also confer its carrier with resistance to malaria. Whether its a beneficial mutation depends entirely on the environment, from prevalence of malaria to availability of treatment for the various symptoms.