Apply more varnish to that spot to see if it goes away. It could be that you need more varnish to fill it in properly so that light doesn't diffract through it differently than the rest of the bpat. If that doesn't work and it still bothers you, sand down to the scratch using something like 120 grit, sand the scratch with 240 grit, then build the varnish back up.

It's my bet that this works.

Robert N Pruden