The death of a 4-year-old boy whose body was set on fire and found in a vacant Englewood home last month has been ruled a homicide.

Manuel Aguilar was discovered Aug. 2 in the 1400 block of West Marquette Road. An autopsy found his death was the result of probable neglect, and was ruled “homicide by unspecified means,” the Cook County medical examiner’s office announced Wednesday.

His mother, 27-year-old Alyssa Garcia, was charged with felony counts of concealing a death and attempted residential arson,police said. Also charged were Christian Camarena, 19; and a 17-year-old boy who is related to Camarena and was Garcia’s live-in boyfriend.

Manuel’s malnourished, partially burned body was found by firefighters covered in a charred, blue blanket inside the vacant home where Garcia, her 17-year-old lover and his older brother were seen entering moments before with a container of lighter fluid, authorities said.

Manuel was so tiny, investigators first mistook him for a 9-month-old baby, Assistant State’s Attorney Jamie Santini told Judge Maria Kuriakos Ciesil at a bond hearing.

The firefighters who came upon the small fire in the basement of the two-story house also saw the can of lighter of fluid next to the boy’s body.

A naked Manuel had been discovered dead days before on July 29 in the stench-filled backroom where his mother kept him in the home she shared with her children, her boyfriend and and the boyfriend’s brother, Camarena, in the 6400 block of South Wolcott, authorities said.

When she found her son naked and not breathing, Garcia had one of her other five children check Manuel’s heartbeat and pulse, Santini said. Garcia later told police she tried to resuscitate Manuel by putting his lifeless body in the shower.

Fearing that officials with the Illinois Department of Children and Family Services would take her other children away, Garcia and her boyfriend washed Manuel’s body, put clothes on him, and wrapped him in the towel, Santini said.

Eventually, the couple transferred Manuel’s body into the trunk of a car, Santini said.

When Garcia was finally ready to dispose of the body, she sent her children to stay with family members while she, her boyfriend and Camarena drove a mile away to the abandoned home in the 1400 block of West Marquette, Santini said.

Garcia, who had been working at an Olive Garden, was arrested shortly after she was seen running from the home, Santini said. Camarena and his brother were nabbed behind the building.

Santini said Garcia admitted what she did in a video-recorded statement, and said she didn’t seek medical attention for Manuel or call police because she didn’t want DCFS involved.

Garcia was ordered held on a $2 million bond. Camarena was ordered held on $1 million, and his younger brother was ordered held in custody on the same charges by a Juvenile Court judge, according to the Cook County state’s attorney’s office.