In the absence of a VAT Return, HMRC issue so-called ‘central assessments,’ being their estimate of the VAT due the Return. FA 2007, Sch 24 imposes a penalty if the assessment is less than the correct Return liability, and where the taxpayer fails to notify HMRC within 30 days of the date of the assessment.
It is not enough merely to submit and pay the Return. The taxpayer has to write separately to HMRC to advise of the underassessment.
One Tribunal said:
“We do not consider that payment of an amount to an HMRC bank account alone can constitute notification of an underassessment. We consider that notification requires a positive action to bring to HMRC’s attention that the amount of VAT due for a particular period is more than the amount assessed.”
(see Silvergate Support Services Ltd  UKFTT 0388