What was the value when the flat was registered in your name in Sept 2010? Was it only for cost of undivided share of land and the cost of construction till that date or the entire value of the flat?
In any case, you acquired ownership of the flat as and when the flat was registered in your name in Sept 2010 and not when it was handed over to you for possession. It will be LTCG only but the determination of cost of acquisition is dependent upon the recitals in the sale deed and construction agreement.
You can avail exemption u/s 54, by investing the capital gains in acquiring another house. You can also avail exemption u/s 54F, by investing the entire sale proceeds in acquiring another residential house. Alternatively you can deposit the sale proceeds in Capital Gains Bonds upto Rs. 50 L to avail exemption.