Chances of having some genetic diseases in the child born out of such marriages increases compared to general population. Not necessary that every such marriage will have children with genetic diseases. Traditionally in India , according to our customs , marriage between the families with same Gotra is avoided and there are many other customs also Preventing such marriages. Preferably such marriages should be avoided on medical grounds, if possible. Well these are personal issues and you should take a decision. There are no guarantees that every child born out of such Marriages will have genetic diseases.