Don’t expect the University of North Carolina System to step into the middle of how UNC at Chapel Hill handled a learning specialist who claimed many student-athletes — especially in “money sports” of basketball and football — couldn’t read at a high school level.

That’s the gist of a letter dated May 29 sent to Louis Clark, president of the Government Accountability Project, from Thomas Shanahan, vice president and general counsel of the UNC System.

In a May 6 letter to UNC System President Tom Ross, Clark asked that the umbrella organization overseeing UNC at Chapel Hill delve into allegations of intimidation and harassment, which Willingham blamed for her departure from the university.

Letting her leave, Clark wrote, “makes it abundantly clear that whistleblowers are not welcome at UNC.”

In his response, Shanahan wrote that unless Clark is acting as Willingham’s attorney, under state law UNC “is limited in its ability to comment on specific personnel issues and cannot respond to your questions about actions taken by or against University employees. Related generally to your concerns about treatment of whistleblowers, though, in January 2014, GAP received information from my office and from Joanna Carey Cleveland at UNC-Chapel Hill about internal options for employees to report complaints and concerns.”

Willingham went on CNN, ESPN and HBO, alleging that she had data demonstrating that 68 percent of 183 student-athletes tested at UNC couldn’t read at a high school level when they reached college. She also talked about so-called “paper classes,” which rarely met and only required students to submit a term paper by the end of the semester.

Chapel Hill administrators asked three external academics to review the data and determine whether her findings were valid. All three cast doubts on the work of Willingham and her team.

Shanahan cited the facts that the reviewers weren’t from North Carolina and had no ties to UNC at Chapel Hill as proof that they gave independent assessments.

“Based on my review of your letter and UNC-Chapel Hill’s response, it is clear that the University has provided a great deal of information about its reviews, both to you and to the public, and has otherwise responded to your inquiries,” Shanahan wrote.

Clark also asked about the independent investigation by Ken Wainstein, a former U.S. Justice Department official, into academic irregularities at Chapel Hill.

“Mr. Wainstein is conducting an independent, comprehensive investigation,” Shanahan wrote. “Consistent with the independent nature of the investigation, President Ross and [UNC-Chapel Hill] Chancellor [Carol] Folt do not direct or oversee the details of his work.

“Mr. Wainstein has the discretion to direct his investigation in whatever way he deems necessary. How he proceeds, how long it takes, to whom he talks, and what questions he asks are entirely up to him.”

Shanahan added that UNC looks forward to receiving Wainstein’s report, which will be made public. Folt said at a recent board of trustees meeting that she thought it might be finished sometime this summer.

Officials at the Government Accountability Project could not be reached for comment late Monday.