Nucleo STM32L4 non blocking timer within interrupt

Question

I am using an STM32l4 nucleo to integrate my project. My aim is to toggle a pin after an interrupt occurs with a 5 ms delay. Below is the implementation in my code

void EXTI1_IRQHandler(void) {

    if(k==0){
        timestamp1 = HAL_GetTick();
        k=1;
        flagk=true;
    }else{k=0;}

    HAL_NVIC_ClearPendingIRQ(EXTI1_IRQn);
    HAL_GPIO_EXTI_IRQHandler(GPIO_PIN_1);

}

and inside my main

while(1){
        //timestamp1 = fReturnTimestamp1();
        Timestamp2=HAL_GetTick();
        if((Timestamp2-timestamp1)<margin){
            HAL_GPIO_WritePin(GPIOA,GPIO_PIN_11,GPIO_PIN_SET);
        }else{
            HAL_GPIO_WritePin(GPIOA,GPIO_PIN_11,GPIO_PIN_RESET);
        }
    }

The margin is 5ms. The problem I'm encountering is that when I connect an oscilloscope to the toggle pin, the signal isn't stable. There's a random difference of about 1 ms.