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Hi. My name is*****'m looking at your question now and will post my answer or ask for more information here in a short while.
Have you ever owned a property which was your previosu main residence and which was either sold or become part of your property portfolio? If so, when was it sold exactly or if you kept it when did you move out?
In the scenario you set out, you will pay the higher rate of stamp duty as you won't have replaced your previous main residence ( a rented property is not a main residence for this purpose). However, if you sell what is now your main residence within 36 months of buying a new main residence, then you will be able to claim a refund of the 3% excess stamp duty. Take a look at the original consultation document and the consultation results document here.
I hope this helps but me know if you have any further questions.