Would like to consider a new 'no call region' component for the region-studied profile. With this component, in response to a query for variants in a given region, a server can provide a report that also enumerates non-callable subregions, potentially enabling one to differentiate non-callable vs. true negatives.
 
(The main use case we based this on was the need to include wildtype variant calls for PharmGKB's PharmCAT (https://github.com/PharmGKB/PharmCAT) software).
 

The attached example is a set of variants found for 1000 Genomes patient HG00403 in range chr1:1000000-1100000 that includes non-callable subregions. (It's based on a slightly outdated pre-publication version of the IG).