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By Mary Emily O'Hara

The U.S. Department of Health and Human Services (HHS) suggested late on Tuesday that it may soon make changes to a nondiscrimination rule in the Affordable Care Act (ACA).

Rule 1557 of the ACA mandates states, hospitals and medical providers receiving federal funds do not discriminate on the basis of race, color, national origin, sex, age or disability. More specifically, the rule states sex discrimination covers gender identity and all forms of reproductive care — including birth control and pregnancy termination.

Protesters gather in opposition to the Obama administration's health care mandate for religious institutions in 2012 outside the James A McClure Federal Building in Boise, Idaho.Charlie Litchfield / Idaho Press-Tribune via AP

Because of the abortion-rights provision and the mandate to cover transgender health care, five U.S. states and a group of religiously affiliated health care companies sued the federal government last year.

"This HHS can’t change discrimination based on sex, but they can change the way that sex is interpreted," ACLU Attorney Brigitte Amiri said. The ACLU filed repeated attempts to intervene in the case, known as Franciscan Alliance v. Price.

On Tuesday, HHS filed a document in the case that said it will "reconsider the regulation at issue" and asked for the court to put a hold on the case while it looks into altering the ACA's nondiscrimination rule.

"A remand would permit HHS to reconsider the challenged aspects (or other aspects) of the Rule in light of its desire to assess the Rule's necessity, reasonableness, and efficacy — or lack thereof," the HHS document stated.

Transgender advocates were especially concerned by the news. Currently, the only federal policies that define anti-transgender bias as sex discrimination are the ACA rule and the Violence Against Women Act.

“The Section 1557 regulation has been literally life-saving for transgender people all across the country, who are routinely turned away from emergency rooms and doctors’ offices and refused coverage for critical medical care," National Center for Transgender Equality Executive Director Mara Keisling said in a statement emailed to NBC News.

"The administration is rejecting the views of every major medical associations, most courts, and most Americans, who believe that people should not be denied health care because of who they are," Keisling added. "That’s not just bad science and bad law — it’s a dangerous attack on transgender people’s ability to survive."

NBC News reached out to the HHS for comment on Tuesday but did not receive a response before publication.

Transgender people frequently face obstacles when seeking basic health care. In 2015, for example, the community spoke out using the hashtag #TransHealthFail to describe doctors who turn them away for medical issues as common as a head cold. And the obstacles to health care aren't always due to bias — many in the health care profession have little training when it comes to transgender health and assume that health issues arise in connection to hormone use or other gender-related care.

Related: Many Trans Patients Face Fear, Stigma at Doctor's Office

“People do think every little malady that you have is because you’re taking hormones and you should just stop that right now. Which is very untrue,” Jamison Green, former president of the World Professional Association for Transgender Health, told the Daily Dot in 2015.

But reinterpreting the ACA nondiscrimination rule wouldn't only affect the lesbian, gay, bisexual and transgender community. The provision that says denying abortion services is sex discrimination impacts all women and girls who rely on insurance coverage for contraception and abortion.

"I don’t know what the substance of those changes will be," Amiri said, but "I’m deeply concerned that they would effectively gut protections for LGBT individuals and people seeking reproductive health care."

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