Doctor scared my son talking about him having congenital malformation. What would you say?

Please see below. Congenital just means 'present at birth' and malformation means it didn't form in the usual way; your son probably knows that that part looks different from his friends. His doctor can talk with you and your son about what impact, if any, this issue will have on him.
Ambiguous term. Ca just means the issue was present at birth. Terminology can be frightening. I doubt your son was surprised to hear the issue was present at birth, since he has lived with it & probably knows it is different.If your son was curious & wanted to know why he was different i think a simple lable was insufficient. Understanding how it came about would be better.Share your concern with the dr.
Limb differences. In the upper extremity we like to call these limb differences it is a much easier term limbdifferences.Org is a resource for families and friends of children with limb differences. And there are many regional support groups such as www.Littlefins.Org little fins limb difference group - a support group of families located in the twin cities, mn area.