The jury in the trial has previously been told Ms Joynes became pregnant by a second child, Boy B, while she was on bail for allegedly having sex with Boy A.
Boy A told jurors he and the teacher exchanged messages on Snapchat and she picked him up after school on a Friday night.
His mother’s statement said her son arrived home, changed out of his uniform and said he was staying at his best friend’s house.
The trial heard Boy A later told police the teacher had warned him, “no-one had better find out” after they had sex at her Salford Quays flat.
His mother said she had been called into school the following Monday and told by police about an anonymous report to Childline, which concerned an allegation involving a teacher and her son.
Her son was called out of class but told his mother, “It was just a stupid conversation in group chats that got out of hand,” and he told police it was just, “friends having banter”.
The court heard she left the school with her son, but got a call later from the mother of the boy her son had supposedly been staying with.
“I think I owe you an apology,” she was told, before the parent confessed Boy A had not been staying at her house – and that she had picked him up from an address in Salford the day after.
The jury heard Boy A’s mother said, “Where did he stay then? It wasn’t at the teacher’s was it?”
She was then told, “Yeah, it was”.
Boy A’s mother’s said: “I was upset and crying at this point. Crying my eyes out.”
She returned to school in “tears”, Det Con James Partington of Greater Manchester Police said in his statement.
“She stormed into reception and I would describe her as in a panic and distraught.”
Ms Joynes was suspended from school as police investigated and she was bailed on condition she had no unsupervised contact with anyone under 18.
She denies two counts of sexual activity with Boy A, two counts of sexual activity with Boy B and two counts of sexual activity with Boy B while being a person in a position of trust.
The trial continues.
