The pupils will now be marked on predicted grades, exams and mocks
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More than 100 GCSE pupils received a last-minute call to sit an exam two weeks early after a mix-up meant they were given the wrong date.
But 20 of 120 students at Ysgol Gyfun Rhydywaun in Aberdare, south Wales, who thought the religious education paper was on 14 June, refused to sit it.
Headteacher Alun Davies said a clerical error had occurred at the school.
Wales' exam director Derec Stockley said marks would be based on the exam, mock exams and predicted grades.
Most of the pupils were taking a short-course version of the GSCE, which is exam-based.
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We will do everything we can to ensure pupils are treated fairly
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Students sit one of two exam options - A or B - with option A scheduled for Friday, 27 May and B scheduled for 14 June.
The mistake led to the Ysgol Rhydywaun pupils being entered for the wrong paper, meaning they had the wrong date.
Pupils were contacted when the error was discovered on Friday morning, and the exam was allowed to be delayed until that afternoon.
Mr Stockley, director of examinations and assessment for the Welsh Joint Education Committee (WJEC), said: "They had been wrongly entered for option B rather than option A. It was a clerical error at the school.
"We were informed when an examinations officer at the school called one of our examinations officers just after nine o'clock.
The exam was moved to the afternoon so students could sit it
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"The school phoned 120 pupils to try to get as many into school to sit the exam.
"Those who sat and those the school failed to contact will get special consideration to ensure they are treated fairly and get a result that would have been the expected result because, obviously, it's not their fault."
Mr Stockley said the school was investigating how and at what point the mistake was made.
"It's a rare occurrence but there are so many examinations now that one can understand why human error comes in," he added.
"We will do everything we can to ensure pupils are treated fairly."
Headteacher Mr Davies said the error had been made at the school but not by the examinations officer.