I realise that this area has been covered here before, but this situation is slightly different.
HMRC issued 2007/08 return in June 2012. Tax return submitted within 3 months of the issue date. It shows a repayment due. HMRC decline to process the return and so deny the client the repayment. HMRC quote the 4 year deadline for the return as running out on 5.4.12. However, isn’t the deadline the later of 5.4.12 or 3 months after the issue date of the return?
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Just to check - the self-assessment return was issued for the first time in June 2012 and this was not a duplicate return as HMRC should not have issued new 2008 returns after December 2011.
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If there was tax due they would have accepted it quite happily.
If its a repayment then it is out of time.
http://www.hmrc.gov.uk/briefs/brief1610.htm
I did post previously about claiming losses from out of time periods (to roll forward on BTL) and didn't get any response about any ways around it, ie trying to claim this was careless doesn't seem to give you 6 years.
At a loss to understand why HMRC have even issued this return, although probably just down to staff not knowing their own regulations.
I would write again pointing out that the return should not have been issued after 31 December 2011 BUT as it has been then it should be processed & repayment issued. as it has been filed within the three month deadline.
Good luck.