The rate would depend whether the project started after 1.4.19 or before this date if the project was started before this date then the builder will have an option to choose from 12% rate and 5% rate and if he has chosen 12% rate then he will charge you that but if the construction started after 01.04.19 then he needs to compulsorily charge 5%. It doesnt matter when you have booked the flat it depends on which scheme builder has chosen.
GST will be charged on value charged for constructing your property which is same as agreement value.
What else is included in your agreement value? Are there any amenities?
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