The court also directed the Tamil Nadu government to issue guidelines to streamline the procedure for appointment of transgenders in its services.
Justice N Kirubakaran gave the directions while disposing of a writ petition by Tharika Banu, a transgender.
The Judge allowed the 27-year old's plea seeking allotment of a BSMS seat for academic year 2017-18.
In his order, the Judge said the petitioner's claim for admission to the course cannot be denied on the ground that she has not obtained the minimum 50 per cent marks.
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"Therefore, leniency should be shown to the transgender person," the judge said.
Authorities were guilty of not implementing The Supreme Court and High Court orders to provide reservation for them, the court said.
The petitioner should be admitted in the course within a week, failing which the authorities shall appear before it on December 11, the court directed the secretary, Directorate of Indian Medicine and Homeopathy.
Referring to the plight of transgenders, the judge said they faced harassment, sexual violence and were denied basic civil rights.
He hoped that this order would be the first step to throw open the doors of educational institutions for the entry of transgenders for their social empowerment, employment, dignity and rights.
He said such rights have been denied to them till date, violating the fundamental rights guaranteed under the Constitution.
The judge also directed the state to issue guidelines on the "determination of the community" and "reservation in employment" for transgenders.
He directed that procedures to be followed by state agencies in selecting the third gender candidates for appointment in its services be streamlined.
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