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In the variant search page, open the search panel. This should have one blank field. Click the 'common filters' and add a field. The existing blank field is retained - we should probably remove it.
Do the above and hit submit. The first blank filter turns red because it's invalid (that's correct). however, when you remove it, the second (valid) filter gets shifted to spot 1 and it now turns red. We should re-calculate the valid status when changing filters.
Do the above, clear the blank filter and apply. Now re-open the filter dialog. When applying a new 'common filter', it replaces the existing, rather than appending. I'm not sure why this would behave differently from the above; however, we should probably append to existing non-null filters, rather than replace them.