Hi Annie, this is a fantastic question.
I’m actually writing something on this subject for this website but that might take a while. In the meantime I’ll give you some notes on what I think may help.
1) Our brains appear to have an issue with sensory gating. Specifically we don’t seem to be able to filter out (ignore) certain everyday sounds that form background noise or a mild annoyance for neurotypicals.
2) We know that these specific sounds trigger activity our amygdala, the warning centre part of the brain often ascribed to ‘free-fight-flight’.
3) All of this is pre-conscious in the sense that we don’t get to choose to ignore these sounds or halt that rush of sensation (cortisol the stress hormone etc) which can lead to a feeling of panic and so on.
If I were a betting man I would say that misophonia may turn out to be a form of synaesthesia.
This is a very basic summary, and there’s a lot more to it, but hopefully it will give you a bit of an idea!