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Your employer explained it incorrectly. The fact is that you have an interest free loan which you won't get from a commercial lender. That is why you have a taxable benefit in kind at 3% on which you will pay a maximum of 20% tax if you are a basic rate taxpayer, 40% if you are a higher rate taxpayer and 45% if you are an additional rate taxpayer. It's no different to a company car benefit. You get a nice car to drive with no running costs except fuel and you don't have to use your own savings or borrow at commercial rates to buy your own car, hence the taxable benefit in kind.
I hope this helps but let me know if you have any further questions.
Take a look at the official rate of interest history here. Its not based on deposit rates. It's based on lending rates.
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