Just because a virus genome is small doesn't make it simple, actually quite the opposite (think of it as an obfuscated, compressed package, that is hugely variable with no checksum). In the case of this virus there are even overlapping open reading frames, which is something you would never find in a eukaryotic genome, and almost the entire genome is protein coding, whereas only 2% of the human genome is protein coding.

The real value of AlphaGenome is not the effect of SNPs on protein coding regions (there are other tools for that, like AlphaFold), but rather identifying regulatory elements, such as promoters or alternative splicing patterns or microRNAs, within the ~98% of the genome that hasn't been well characterised yet.

That 98% is vastly underexplored, so a tool like this could help researchers interested in expression profiles or alternative splicing patterns of a protein, identify the source. Obviously not every "important" SNP will be consequential, but it helps narrow the search for that needle in a haystack.