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The 33-year-old Uruguayan used the term "negrito" when replying to a friend's congratulatory post following his two goals in Manchester United's 3-2 victory over Southampton in the Premier League in November.
United insisted that Cavani was unaware of the negative connotations that the word carries in Britain, as he intended to use it as "an affectionate greeting".
The striker deleted the post and apologised. But English football's governing body claim that the post constituted "an aggravated breach" of FA Rule E3.2 due to the reference to colour, race and/or ethnic origin.
Cavani and his club have until Monday 4 January to respond. This means the attacker will be available for all of United's Christmas and early new year fixtures, before facing any disciplinary action.
United issued a statement following the news making it clear they will back their player, but are waiting to consider their options before issuing a response to the FA.
The Old Trafford club's statement read: "Manchester United and all of our players are fully committed to the fight against racism and we will continue to work with the FA - along with other governing bodies and organisations, and through our own campaigns - in that regard.
"We note the FA decision today to charge Edinson Cavani for his social media reply to a friend's message of congratulations following the Southampton game.
"Edinson and the club were clear that there was absolutely no malicious intent behind the message, which he deleted and apologised for as soon as he was informed that it could have been misconstrued.
"The player and the club will now consider the charge and respond to the FA accordingly."
The FA's statement read: "Edinson Cavani has been charged with misconduct for a breach of FA Rule E3 in relation to a social media post on Thursday 29 November 2020."
All imagery: PA Images
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