The short answer, explained
If your taxable turnover passed the VAT registration threshold and you didn't register on time, HMRC treats this as a failure to notify.
It can then backdate your registration to the date you should have registered, charge VAT on sales from that date, and add a penalty on top calculated as a percentage of the VAT that went unpaid because you registered late.
How much you pay depends on why the registration was late, whether you told HMRC yourself or it was found in a check, and how quickly you cooperated once it came to light.

