Genomic Variants
After clicking on the Gene tab, use the left side menu to select Variant table under the category Genetic Variation.
Note: this will be a VERY large table, so give it time to load, then filter by minor allele frequency, SIFT or PolyPhen scores, or consequence.
Similar to filtering at the transcript level, click on Consequences at the top of the table and select your consequence filters.
This table is virtually identical to the table you saw at the transcript level, but it also includes an extra column at the right: the transcript column. This will tell you which transcript the variant is observed in. The same variant can be depicted multiple times in the table, for each transcript in which it is observed.
The Gene tab's Genetic Variation menu also includes Structural variants: insertions, deletions and larger structural variants.