The Long Island Rail Road’s longtime anti-fraud custom of listing “M” and “F” genders on fare cards discriminates against transgender people and should be stopped, according to the New York City public advocate.

In a letter last Monday to Metropolitan Transportation Authority head Veronique Hakim, Public Advocate Letitia James says the gender policy “violates the spirit, if not the letter” of state and city laws meant to protect human rights.

To deter sharing of passes, purchasers of some multiuse tickets must pick either male or female, clerks selling tickets at rail booths determine a purchaser’s gender based on appearance, and train employees might not honor passes in cases of mismatch.

“This unnecessary, antiquated, and reductive system poses serious constraints on a range of groups, including transgender individuals, those whose dress or appearance is gender-nonconforming, and anyone who doesn’t feel their gender is relevant to riding public transit,” wrote James, who also wants the MTA, which runs the region’s transit system, to abandon the practice where applied on subway and MetroNorth passes.

The MTA’s chief spokeswoman, Beth DeFalco, said: “We want every customer to feel welcome on our system and this ticketing change is one we have been actively exploring implementing, especially as we transition to new fare payment systems and increased use of electronic ticketing.”

At the very least, the MTA should add a third option, said Cynthya Briankate, 40, of Ridge, who was raised a boy, transitioned about two decades ago, and identifies as transgender and intersex, which means biologically between male and female.

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“We have a Long Island Rail Road that seems to be pigeonholing people based on what sex is listed on their legal paperwork,” said Briankate, who prefers feminine pronouns. “I do not feel my body is 100 percent of either.”

Chicagoland’s Metra system removed gender from passes in 2015. Philadelphia’s SEPTA railway agreed in 2012 to stop affixing gender stickers to its weekly and monthly passes, following yearslong pressure by LGBT activists. And in India, “a transgender/third gender” was to be added last year to railway reservation options after a lawsuit.

Katie Haag of Long Beach, who is not transgender, said although the issue didn’t impact her personally, she is not opposed to tickets being gender neutral.

“I never understood why it had to be ‘male’ and ‘female’ on the ticket,” the 20-year-old waitress said Saturday while delayed at Penn Station, holding an “F”-branded pass. “It just seemed pointless.”

There are about 1.4 million transgender adults in the United States, about 0.58 percent of the population, according to the Williams Institute, a policy center at UCLA Law School.

With Deborah S. Morris