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The 2015 tax return was due for submission to HMRC by 31 January 2016. One day late and you are fined £100. If the tax return was still not submitted by 30 April 2016, then a £10 per day penalty is charged for up to 90 days. After that, another £300 penalty or 5% of any tax unpaid whichever is greater is added. If the tax return is a year later, another £300 penalty is added.
I have had new clients come to me with problems such as these. Last year, I appealed against 4 penalties and all of them were accepted and the penalties cancelled due to HMRC taking a more lenient view especially when no tax was paid late or no tax was due at all. If your son did not owe any tax for 2014/15 as at 31 January 2016, the due date for payment, then he has a good chance of having his appeal accepted. Have your son complete the appeal form here. If I were him, I'd cite his being new to self-assessment as one reason for being late with the return. As he owed no tax, use that fact as another reason for appealing.
By being late with the tax return, he could have delayed the tax payment he needed to make which would have given him an advantage over taxpayers who paid on time. This is how HMRC look at it. As he owed no tax for 2014/15, there has been no loss to the Treasury.
I hope this helps but let me know if you have any further questions.