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This is a tricky situation. Your son is 3 months now. Watch for the next 2 months. If he still continues to have clonus, you should suspect some abnormality.
Presently, it appears he falls in the normal group of infants who have ankle clonus. Just observe if he gets the clonus different positions.
A study about clonus in infants revealed that about 58% were normal children, when there were no other clinical symptoms .
Hope for the best.
Regards
Thanks Abhijeet, now my son is 5 months old. Luckily his ankle clonus dont appear anymore. He has started rolling over, maintains very well in prone.