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I think it means the genital defect is normally rare, but is much more common in these kids?

Even .24% isn't that rare.

From NIH.gov:

"In the United States, a rare disease is defined as a condition that affects fewer than 200,000 people in the US."

That works out to 6.0341E-06%

A condition which would affect 6e-6%, or 0.000006% of the US population (330M) would affect 20 persons. 200000/330M = 0.0006 = 0.06%.

The deformity in the general population affects 0.24% of male babies, so 0.12% of the population.

GGP is still 4 orders of magnitude off.