I find the disambiguation of terminology based on normal vs abnormal function to be more useful than the one based on the arbitrary 1% frequency of the least common allele. As your citation in #msg-75807204 notes with respect to the sickle-cell gene, classifying by function is not entirely clear-cut; however, normal vs abnormal function would seem to provide a reasonable workable definition for the terminology in almost all cases without the need for employing an arbitrary frequency threshold.
I think that's the crux of the issue.
Most polymorphisms have not been examined for function. They're reported into the literature often by investigators who do not have an interest in defining the impact of the specific polymorphism.
Under your criteria, most polymorphisms would be neither normal or abnormal but rather undefined.
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