The Trump administration’s expansion of religious exemptions is undermining civil rights protections and codifying discrimination against marginalized groups — particularly LGBTQ people — according to a report released Monday by three research and advocacy groups.

Using a combination of new rules, legal interventions and newly created divisions, the departments of Health and Human Services, Housing and Urban Development, Justice, Labor and State have all taken steps to advance “religious liberty,” often at the expense of LGBTQ rights, the American Civil Liberties Union, the Center for American Progress and the Movement Advancement Project argue in their report.

“When you connect the dots, you really see the administration pushing for a sea change in our culture and legal norms … at the expense of existing nondiscrimination principles.”

LOUISE MELLING, ACLU DEPUTY LEGAL DIRECTOR

“The many proposals to allow religious discrimination are consistent with the trend of the administration to undercut civil rights broadly,” Louise Melling, deputy legal director of the ACLU, told NBC News. “The administration is taking the position that religious freedoms give you a right to discriminate.”

The White House disagreed. Spokesman Judd Deere accused the organizations of being “a campaign arm of the Democratic Party” that has “refused to credit the President with any action he’s taken to protect LGBTQ Americans.”

“The President believes in human dignity for all and that no one should be discriminated against, including religious organizations and the LGBTQ community,” Deere said in a statement. “These actions build on President Trump’s longstanding commitment to responsibly safeguard the fundamental right to religious freedom by eliminating unfair and unequal treatment by the Federal government.”

Empowering or ‘harmful’?

Following Trump’s May 2018 executive order establishing the White House Faith and Opportunity Initiative, a measure to empower faith-based organizations and “promote religious freedom,” government agencies submitted nine proposals to the Federal Register to revise how they distribute federal funds to religious organizations to reduce poverty.

The proposed rules — from the departments of Justice, Health and Human Services, Labor, Housing and Urban Development, Veterans Affairs, Homeland Security, Agriculture and Education, along with the U.S. Agency for International Development — would undo several Obama-era regulations, including those that require federally funded religious organizations to inform beneficiaries about certain rights.

For example, if a homeless LGBTQ teen sought help from a faith-based provider and the provider was not accepting of the teen’s sexual orientation or gender identity, the provider would no longer have to inform the teen under the new rule about alternative providers that may be more accepting.

“These rules would be harmful to LGBTQ people, women, religious minorities and others during the best of times, but they’re particularly unconscionable during a public health crisis when even more people than usual are relying on social services,” said Rachel Laser, president of Americans United for the Separation of Church and State, which was not involved with Monday’s report.

‘Clashes of rights’

Aside from rule changes or proposed changes stemming from Trump’s executive order, advocates point to several other measures at major federal agencies that they say advance religious freedom at the expense of LGBTQ rights.

In October 2017, the Justice Department issued guidance directing all executive departments and agencies to prioritize “the foundational principle” of religious liberty. A year later, Jeff Sessions, then the attorney general, created the Religious Liberty Task Force to implement the guidance across the federal government.

The Justice Department also made the government’s position on potential clashes between religious liberty and LGBTQ rights clear inlegal briefs, including one to the Supreme Court, where it sided with Jack Phillips, a Christian baker who refused to make a wedding cakefor a same-sex couple.

A Justice Department representative said the agency has invested in defending the rights of LGBTQ people, most recently in a case in Puerto Rico involving the shooting deaths of two transgender women, Layla Peláez and Serena Angelique Velázquez.

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Secretary of State Mike Pompeo created the Commission on Inalienable Rights in July. LGBTQ advocates questioned the purpose of the new commission and criticized its chair, Harvard professor Mary Ann Glendon, for public comments she had made opposing same-sex marriage.

A State Department representative defended the commission and its members, saying: “No member would think that because of a person’s sexual orientation they would have fewer or more constrained rights than anyone else.

“Mary Ann Glendon has argued that as a matter of fact there are clashes of rights,” the representative added, but the commission “doesn’t consider it part of its mandate to resolve these controversies.”

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At the Department of Health and Human Services, the director of the Office of Civil Rights, Roger Severino, created the Conscience and Religious Freedom Division in January 2018 and later changed his office’s mission statement from explicitly ensuring equal access to HHS services to emphasizing the protection of religious liberty.

“The president has been a champion for religious liberty from the moment he stepped into the Oval Office, and we have been following his direction to ensure protection of religious liberty,” Severino told NBC News.

Responding to the argument that expansive religious freedom constitutes a right to discriminate, Severino said: “Everyone has a fundamental equality and dignity by nature. In a pluralistic society we are going to have all sorts of views on important issues that affect people, and we have to live together in an environment of mutual respect.”

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In May 2019, the HHS proposed a rule to roll back nondiscrimination protections in the Affordable Care Act and to expand the religious exemption by broadening the range of entities that would be exempt from the nondiscrimination provisions. It finalized a health care refusal rule that would broaden the ability of health providers to refuse to provide particular medical services because of religious or moral objections. Then, in November, HHS proposed a rule to allow foster and adoption agencies to turn away same-sex parents. That was after HHS granted a waiver to funded foster care agencies in South Carolina to deny services to same-sex or non-Christian couples.

“We have granted relief to faith-based adoption agencies who merely want to continue to do what they have done for decades, and that is to provide forever homes to children by working with folks using their own language of faith,” Severino said.

In August, the Labor Department proposed a rule to allow religious organizations that contract with the federal government to fire employees who do not follow the tenets of their faith, even if doing so amounts to discrimination on the basis of sexual orientation and gender identity.

The Labor Department said the rule was proposed to provide “the broadest protection of religious exercise” for companies that compete for federal contracts.

The Labor Department did not immediately respond to a request for comment.

‘Pushing for a sea change’

Other changes may be on the horizon: Following Trump’s Presidential Executive Order Promoting Free Speech and Religious Liberty, which asserts the right of religious organizations to practice their faiths, the Office of Management and Budget mandated that all federal agencies detail how they would distribute federal grant money in compliance with the order.

Severino said the measure is designed to ensure that “the dollars we send out are not used to discriminate against people because of religious denomination or faith,” but an HHS representative said the agency had no plans to publish any new policies as of last Friday.

LGBTQ rights advocates, however, fear that the measure could channel government money toward organizations unwelcoming to LGBTQ people, and they are calling for more transparency about how federal agencies plan to administer their grants.

“We don’t know how agency staff are being instructed to evaluate grants and the ways this could shift resources and funding away from recipients who comply with nondiscrimination requirements,” said Sharita Gruberg, director of policy for the Center for American Progress, a liberal think tank.

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Gruberg said a coalition of progressive organizations, including hers, plans to file a request under the Freedom of Information Act for any documents related to policy changes as a result of the executive order and OMB’s mandate.

“It’s alarming that something so massively impactful that will affect billions of taxpayer dollars is being handled so secretively,” she said.

For Melling of the ACLU, the number of proposed rules and policies would amount to a sea change.

“Each one of these rules is significant, but when you connect the dots, you really see the administration pushing for a sea change in our culture and legal norms and realities, and it’s a sea change at the expense of existing nondiscrimination principles,” Melling said.