A picture would help, but here is what I've experienced.
At age 3 Raven developed a "tooth bump" on her left side but it wasn't on the bottom of the jaw pointing down, it was on the side pointing outward. I had NO idea what it was but it was about the size of a large marble when I found it. I took her to my normal vet (an equine only facility) and since they said surgery was the treatment, I took her to the university a couple hours away for a second opinion. The said the same thing.
In her case, it was a tooth coming in that didn't have proper room - OR it was a tooth knocked sideways from a previous injury, couldn't say for sure - but it needed to come out and the surgery was because they were going to have to drill a quarter-sized whole in her jawbone to get the "root" out. Both vets said the same thing...they expected to see it on the other side also if it was a true conformation/genetic issue, but since it was only on one side (and never did happen on her right) it was probably from a kick. Yours sould like a typical case of just not enough room for all the teeth - which happens a lot with minis since their heads/jaws are so small.
I had the surgery done in June of that year. She had a gapping hole in her lower jaw that had to remain open during healing. They told me her show days were probably over. I was devasted. But by late July she was totally healed, eating normally and the scaring was minimal. She went on to win two World titles and one National title that fall! I was SO relieved! I believe the cost was around $1800.
My understanding is that root has basically fused with her jawbone. So they used a drill and a sanding-type tool to sand down the bump because her jawbone had grown into that convex shape because of that sideways root.
Maybe if you jump on this early you will find it's either something totally different (although being on both sides I bet it's a sideways tooth) or it may cost a lot less to resolve.
Good luck and please keep us posted.
BTW, I was told to keep a close eye on Raven as she matured as they thought if it wasn't a kick it could materialize on her right side also. She's five now and still no sign of any other issues.