Neither sentence is correct. You mean "a genius" (where "genius" is a noun).
(1) I regret not being a genius. (2) I regret that I am not a genius.
The structure used by (1) refers to the past (compare: "I regret not being a Boy Scout when I was a kid"), whereas the structure used in (2) refers to the present. If you mean what (1) means, (1) is correct. If you mean what (2) means, (2) is.
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