Welcome back to the Forum. I'll try to provide some information but the real thing that needs to be done is that your son needs to see a dermatologist and find out what this is and have it taken care of.
The lesion you describe sounds nothing like genital herpes and if it were, the lesion would have healed in just a few weeks, not have persisted for several years. In the location you describe there are a number of absolutely normal things which could be present- cysts, infected hair follicles, etc. Alternatively, but probably less likely , this could be a genital wart. None of the possibilities I have mentioned are a big deal- they are easily treated if treatment is needed and have little long term harm. As far as a cancer is concerned, if this were a cancer, it would be expected that it would have gotten bigger or otherwise evolved over the years of observation. Chances of cancer are small. Even if it were a concern, the thing to do would be to get it treated (typically with very simple, office based surgery) which would be curative.
No matter what this is, it does little good to wait and worry. Urge your son to not worry and to seek the opinion of a dermatologist. EWH