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Vaccines can have devastating permanent side effects. Should parents no longer vaccinate their children?
The answer for both is:
Whichever option does less harm should be taken. A delayed puberty, despite potential long-term risks does less harm than a trans child going through the "wrong" puberty.
Besides, due to the start of puberty having a pretty large range there should in theory be little harm until the age of 14 or so. And at that age children are much more capable of deciding on medical treatments than as preteens.
The main difference with vaccines is the overwhelming medical proof of the benefits, that's something that currently isn't there with the use of puberty blockers during the years you would typically go through it.
I do somewhat agree with your less harm premise. If a child literally threatens to kill themselves, then as a parent you'd feel like you had little choice in the matter, however if there are permanent side effects and the child, now as a young adult starts regretting their decision, it's going to be shit for everyone.
There is significant proof of benefits:
https://doi.org/10.1111/camh.12437
I can't vouch for the quality of this literature review (because I don't want to take an hour or more to read a paper for a Lemmy comment), but usually literature reviews show a fuller picture than individual studies.
Also, this sentence is in the conclusion: