Santander wrote to those affected this week informing them the change will take place from 3 October this year.

A Santander spokesperson said: “We also told customers that we intend to increase our SVR Cap margin – the maximum amount above the Bank of England base rate that we can charge – from 3.75% to 4.99% from 24 September.

It said the move was prompted by the rising cost of mortgage provision and savings rates.

“Additionally, the cost of running a bank in the UK has increased dramatically through a combination of increased liquidity, capital and funding requirements.”

Halifax was the last substantial lender to increase its rates to 3.99% in May, after a 0.49% increase affecting 850,000 borrowers. Bank of Ireland also announced a two-stage SVR hike before that, from 2.99% to 3.99%, with a final rise to 4.49% next month affecting 100,000 customers. ING Direct, Yorkshire/Clydesdale Banks and Co-operative Bank also increased SVRs this year and RBS made changes to its offset loans.

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Santander’s SVR mortgage holders will see an average increase of £26 per month for a £100,000 mortgage and offered a mortgage calculator to work out new monthly payments and a customer helpline number for concerned borrowers on 0845 600 0346.

The lender said: “We will consider all particular customer circumstances that might lead to financial difficulties as a result of this change.  We will work with our customers on an individual basis and we have developed a programme to help them manage any impacts – consisting of payment holidays, waiving charges or even resetting mortgages as appropriate.”