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At the behest of Ald. Charles Bernardini (43rd), the Chicago City Council waived tens of thousands of dollars in permit fees on a dormitory DePaul University is building on its Lincoln Park campus.

The waiver, approved by the City Council in September, states that the seven-story building will be used “exclusively for not-for-profit and related purposes” and shall not be leased with a “view to profit.”

But the university–according to its own plans submitted in August to the city’s planning department–intends to lease at least two floors of the building to retailers, possibly a large grocery chain.

The council-approved waiver, at the heart of a complex tale meshing government and development, has allowed DePaul to avert more than $43,000 in permit fees, according to city officials.

Bob Janis, DePaul’s associate vice president in charge of construction, said that when university officials requested the waiver in August, they did not have a lessee for the proposed retail space. They still do not have a tenant.

“If we strike a deal with a retailer, we would go back through the process, and if that meant we’d have to reimburse the city, we would do that,” Janis said. “We are very well aware of how the language reads in the ordinance and it would not be smart to dodge out on that.”

That language, though, also states work on the building “shall be done in accordance with plans submitted.” And those plans include two floors of retail space, meaning the university pursued the waiver even as it drew up a contradictory proposal.

Janis said DePaul elected to opt for the waiver first, and then repay it if necessary, because “it is extremely hard to secure reimbursements from the city.”

He defended the waiver by saying “it is conceivable that we could wind up occupying the entire building ourselves.”

But that statement seems to run counter to what DePaul officials–and the public relations firm hired by the school–have been telling the community over the last year. They have repeatedly told Lincoln Park neighbors, many of whom oppose the height of the building, that the school needs at least two floors of retail to make the structure monetarily feasible.

“For that building to be economically viable, the retail needs to be there to support the building,” said Tom Coffey of the Haymarket Group, a public relations and political consulting firm.

Representatives from DePaul, the Haymarket Group and several neighborhood leaders have interviewed two prospective supermarket chains interested in the space, Janis said. School officials have used the possibility of a supermarket as a selling point to the community.

Permit fee waivers such as the one obtained by DePaul are not uncommon. The City Council grants hundreds each year to non-profit agencies such as hospitals, schools and community groups. The waivers–which are sponsored before the City Council by the area alderman–allow the institutions to skirt numerous city permit fees, including building, transportation and water and sewer charges.

The DePaul waiver comes at a time when the City Council and Mayor Richard Daley are under increasing fire for the favors they dole out each year.

In the case of the DePaul building under construction at the corner of Sheffield and Fullerton Avenues, the ordinance passed by the council waives city permit fees, and water and sewer inspection fees.

On Oct. 31 the city’s Department of Buildings waived a permit fee of about $24,000 on the project, according to a spokesperson with that office. Last month, the Chicago Department of Transportation waived a $19,830 fee for construction of a pedestrian canopy the university built when it began construction on the site, a spokesman said.

Bernardini aide Dee Brody, who handled the waiver, said DePaul’s Janis approached her in July and asked that the alderman support a fee waiver on the building. Brody said she knew then that the school planned to use two floors for retail.

“Since there were no leases signed, it seemed there should be no problem waiving the fee,” Brody explained. “If something is built under the auspices of for-profit, then we would assume they would go back and pay the fees.”

But Brody said the alderman’s office is not responsible for policing the university to ensure the money is repaid if the space is leased out.

Brody agreed with Janis’ assertion that getting city reimbursement is difficult.

“The refund process through the city is very slow and in the meantime, the school could use those dollars for better purposes,” Brody said. “I think this is the most expedient way to do it.”

Nina Cadsawan, with the city’s Law Department, said the city would revoke DePaul’s waiver “if the Law Department receives evidence of non-compliance.”

Construction of a seven-story building has irked some Lincoln Park residents who believe it is too tall for the neighborhood. They say it will amplify noise from the elevated trains and transform their back alley into a resonance chamber.

And last month, the city forced the university to halt construction after a city inspector found DePaul was exceeding the limits of its building permit.

Workers were erecting 15-foot columns, which were not allowed under the initial permit. That permit allows only for construction of the foundation and structural supports, but no work at street level.

City officials are considering fining the university for violating the permit order.