If it's at the top of the cleft (in other words, the top of his crack), that does appear, from the way you describe it, to be a pilonidal sinus or dimple, which is a skin feature that can later in life form a pilonidal cyst. The cyst forms when hair (or other debris) and pressure combine in the area to create a tunnel from the pilonidal dimple down into the skin, where a cyst forms that's filled with pus and cellular debris.

The pilonidal dimple is caused by a common defect in fetal development related to the neural tube. The neural tube eventually forms the spine, and is supposed to close after the spinal column is formed. In some people, for whatever reason, the very end of the neural tube doesn't close during development, which causes that pilonidal dimple to form. As far as we know, it's not because of exposure to anything before birth, but rather just a random process that occurs.

For some people, the dimple never forms the sinus and cyst later in life, so it's not a certainty that someone with one will eventually have a pilonidal cyst. The most common time for people to develop one is in their teenage years; mine started around age 16. It'll manifest first as a small hole in the skin that usually leaks blood or pus. If it's caught early, the prognosis is better for removing it successfully. The first sign in my case was blood on my underwear, and my mother could clearly see the hole that it was coming from.

So what I would recommend is to ask your son's doctor to see if it looks like a pilonidal dimple. It sounds like one to me, but since any text description can't fully describe the look and position, I can only speculate on my end. If it ends up being one, you and your son can keep an eye on it and see if anything starts to form over the years. Also note that my needing four surgeries is atypical and kind of a worst case scenario, so it's usually not as scary as my case sounds.