The FA has requested observations from Nottingham Forest, Nuno Espirito, Neco Williams and Mark Clattenburg amid Sunday's penalty drama.
Forest issued a furious statement after their 2-0 defeat to Everton where they were denied three penalties.
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However, the nature of the statement shocked many with suggestions made by the club that Stuart Attwell, who was working as VAR for the game, is a fan of relegation rivals Luton Town.
The club, who have since requested the VAR audio from the game to be released, will be investigated for that and the FA has also asked for observations from their manager Nuno, player Neco Williams and referee analyst Mark Clattenburg.
It's not clear what the request for observations directly relate to with regards to Nuno, Williams and Clattenburg.
The statement read: "We have formally requested observations from Nottingham Forest, Nuno Espirito Santo, Neco Williams and Mark Clattenburg as a result of their comments following their Premier League match against Everton on Sunday April 21.
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"We will provide any further updates in due course."
Meanwhile, the Premier League said: "The Premier League was extremely disappointed to read the comments made by Nottingham Forest on social media yesterday, following its match against Everton.
"We note The FA has confirmed it will be investigating the club’s statement.
"It is never appropriate to improperly question the integrity of match officials, and the nature of these comments means the Premier League will also be investigating the matter in relation to the League’s Rules."
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Moments after the Premier League's statement, Forest said in a statement: "Following yesterday’s match at Everton, NFFC issued a statement highlighting our concern at the perception of the PGMOL appointment of VAR for the game. This was an issue we raised with PGMOL prior to the fixture because of the fear of the side show that would ensue if anything went wrong with officiating in the game. That fear has materialised, as the correctness of three important decisions against the club have been called into doubt.
"This is not about individuals but rather how the integrity of the game is seen. We know match officials do not allow outside factors to influence their decision-making and that all referees are required to declare their ‘allegiances’ to PGMOL to avoid any perceived conflict or harm to the game’s reputation for integrity.
"However, it is clear PGMOL must amend its rule on allegiances to account for contextual rivalries in the league table, not just local rivalries.
"This is currently not within the criteria but should be. Mere reliance on match officials to recuse themselves if contextual rivalries exist invites conjecture, as some have recused themselves where others have not.
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"NFFC stands by its request for greater transparency around PGMOL appointments to further protect the game’s reputation, as intended in PGMOL’s existing approach to allegiances.
"Given the widespread and ongoing concerns, not merely of the fans, players and managers of this club but of many others and the pundits too, over VAR decisions throughout this season any move which boosts confidence in the system should be properly considered."
Forest were left incensed after being denied three penalties they feel they deserved at Goodison Park with Ashley Young escaping punishment following collisions with Gio Reyna and Callum Hudson-Odoi in the Everton box either side of half time.
Young was also spared punishment just before half time when the ball struck his outstretched arm in the Everton box.
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The Toffees went on to win the crucial relegation clash 2-0 with goals from Idrissa Gueye and Dwight McNeil giving them all three points.
The statement from Forest which has sparked the investigation and the Premier League's response, released moments after full time, read: "Three extremely poor decisions - three penalties not given - which we simply cannot accept.
"We warned the PGMOL that the VAR is a Luton fan before the game but they didn’t change him. Our patience has been tested multiple times. NFFC will now consider its options."
And when requesting the release of the VAR audio on Monday, Forest said: "Nottingham Forest has today submitted a formal request to the PGMOL to release into the public domain the audio recordings between officials during yesterday’s match against Everton at Goodison Park.
"The club has requested this be shared for three key match incidents - Ashley Young’s challenge on Giovanni Reyna (24th minute), Ashley Young’s handball (44th minute) and Ashley Young’s challenge on Callum Hudson-Odoi (56th minute).
"We firmly advocate for the broader football community and supporters to have access to the audio and transcript for full transparency, ensuring the integrity of our sport is upheld."
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Meanwhile, Clattenburg hit out at the PGMOL over its 'hat-trick of howlers' during the game.
The result leaves Everton five points clear of the relegation zone, while Forest are just a point above 18th-placed Luton.