If a private individual purchases a second property before disposing of the first, then a SDLT charge arises but is refundable if the individual disposed of the first property within 3 years, if the SDLT isnt paid within 30 days of the purchase of the second property a penalty is raised and interest applied, if the SDLT becomes refundable (although never paid) is the penalty and interest also cancelled as if the transactions never occured or does the penalty and interest remain applicable regardless as to whether the SDLT is refunded, I suppose the question is , is the SDLT cancelled or refunded when the first property disposed of and the second one becomes the only property.
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I can see no reason why it should be cancelled. The amount was payable at the time, and the later refund is of no relevance to that fact.