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“The approach to APR marks the first time in the history of the NCAA that it has ever implemented an academic rule significantly impacting current student-athletes without allowing the members time to adjust to the adoption of the legislation,” Manuel said Thursday.

In seeking the waiver, the school had proposed alternate penalties, including playing a shorter schedule next season, forfeiting the revenue awarded to the Big East for participating in the 2013 tournament and barring Calhoun from meeting off-campus with prospective recruits during the fall 2012 contact period.

NCAA staff rejected the appeal in February, and its Committee of Academic Performance followed suit, and a third appeal was rejected for a third time by the committee’s vice chairman this week.

NCAA spokesman Erik Christianson said schools have known since 2006 that APRs below 900 could result in penalties.

“The same standards are applied to each institution; to ensure all data are comparable for each team, there is a necessary lag time in calculating all the scores at a national level,” he said in an email. “Also, in UConn’s first waiver denial, NCAA staff noted the men’s basketball team’s overall lack of academic achievement and minimal academic progress over several years.”

Christianson also said that “while the Committee on Academic Performance may review policy issues later this year, no changes are expected at this time.”

Manuel would not discuss how the NCAA decision might impact Calhoun’s tenure at UConn. The coach has said he will announce a decision soon about whether he will return for his 27th season at the school.

“Obviously Jim is not happy about it, about where we find ourselves in the men’s basketball program,” Manuel said. “Beyond that, Jim and I have not talked about any impact of this on his decision or my decision or any part of the conversation around whether or not he will be here.

Jim is our coach and Jim is committed to working to ensure that the student-athletes continue to do what they’re doing now.”