You will have to pay IGST first and thereafter apply for refund of CGST and SGST under Section 54 (8) (d) read with Section 77 of CGST Act. Interest is not chargeable as per Section 77 (2) of CGST Act.
Payment of Wrong Tax
Under GST it might happen that the taxable person may pay integrated tax instead of central tax plus state tax and vice versa because of incorrect application of the place of supply provisions. In such cases, while making the appropriate payment of tax, interest will not be charged and the refund claim of the wrong tax paid earlier will be entertained without subjecting it to the provision of unjust enrichment.
Relevant date for applying for refund within two years.
Explanation below sub-section 14
(h) in any other case, the date of payment of tax.
There is no other option.