Please this IRS website for more information: Understanding your CP3219N notice (Notice of Deficiency -- 90-day letter).
You should call the IRS phone number listed on your notice asap to explain your situation and if you have any other options available since you missed your filing deadline.
"Once you receive your Notice of Deficiency (90-day letter), you only have 90 days (150 days if the notice is addressed to a person who is outside the country) to file a petition in the Tax Court. The IRS will accept your past due return, but you may experience significant delays if you file your return after the 90-day period has expired."