Section 56(2)x and section 50c

Hello, I have bought a plot from a person who have not registered it in his name, only have allotment letter from Builder by paying full amount to him. Now i bought it from him and have registered it in my name from builder but my query is , I have bought it a price less than stamp duty value as per mentioned in registery by builder as he has received the same amount earlier, but if i include the premium i paid to the person who have earlier allotment, from whom i have purchased it goes at par with stamp duty value. All payment is made via cheque including premium. In this case does section 56(2)x will be applicable for not.