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Posted by: Jolyon & Katya Ralph
Thinking about this further, although there are some reasons for categorizing agate (and chalcedony in general) as a rock rather than a variety of quartz, there are equally good reasons for keeping it as it is.
It is essentially a 'monomineralic' rock with impurities that can be significant, but the presence of such impurities doesn't specifically exclude it from being regarded as a variety of the mineral species.
For example: sand calcite, desert rose gypsum / baryte all have significant SiO2 included, but that doesn't necessarily mean they should not be classed as varieties of their parent species. Even old favourites such as 'rutilated quartz' are clearly not themselves a rock (they are a component of a larger rock, eg a pegmatite) but are not entirely monomineralic either.
So, we are left with "where does it fit best into mindat?" And at least for now that is as a variety of quartz.