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Chelsea lodged a complaint with the FA over language allegedly directed at their Nigerian midfielder John Obi Mikel by Clattenburg during the home Premier League defeat by Manchester United on October 28.
"The FA has concluded its investigation into alleged misconduct by Mark Clattenburg during the match between Chelsea FC and Manchester United FC on Sunday 28 October 2012. No disciplinary action will follow against Mr Clattenburg," an FA statement said.
However, in a separate statement the FA said Mikel had been charged for breaching its rules.
"It is alleged that in or around the match officials' changing room at the end of the fixture, Mikel used threatening and/or abusive and/or insulting words and/or behaviour," the FA said. "The player has until Friday 30 November 2012 to respond to the charge."
The FA said the evidence for the accusation against Clattenburg had come from Mikel's Brazilian team mate Ramires.
"The details of the allegation were that following one or the other of the red cards issued during the second half of the game, Ramires heard Mark Clattenburg say to John Obi Mikel, "shut up you monkey". John Obi Mikel did not hear the alleged comment.
"Ramires, whose first language is not English, explained that his instinctive reaction was to seek confirmation from John Obi Mikel as to what the referee had said.
"John Obi Mikel, who was being spoken to by the referee, was much closer to the referee than Ramires and did not hear what it is suggested was said to him.
"Three other witnesses, i.e. the other match officials, to whom everything said by referee was relayed via their communication equipment, are adamant the alleged words were not uttered.
"There is nothing in the video footage to support the allegation."
In a statement, Clattenburg, 37, said he was looking forward to putting the incident behind him and concentrating on his refereeing.
"To know you were innocent of something but that there was the opportunity for it to wreck your career was truly frightening," he said.
"Racism has no place in football and this experience should not discourage those to speak out if they genuinely believe they are a victim of abuse. However, there are processes that should be adhered in order that any investigation can be carried out in a manner that is fair for all parties involved."
This month London Metropolitan Police dropped an investigation into a complaint about Clattenburg made by the Society of Black Lawyers following the incident.