In case of refund you have to apply under 119(2)(b) of the income tax act . you have to take approval from CIT to file the return, after approval you can file ( Condonation of delay) income tax return , no interest on refund amount is applicable.
However under 143(1) of the income tax act no refund less than 100/- is applicable so please confirm and then apply under section 119(2)(b) of the income tax act ,