Chakras are real so as Kundalini [0]. However, these aren't physical in nature, rather, they are on subtle body of consciousness. Now, that's not possible to prove scientifically yet, but with your dedicated regular practice, you can experience them yourself as this guy on HN did [1] which inspired me to start my own exploration (back in 2014) and have intense experiences which remains with me.
There's definitely something to chakras. They were always my go to example of a thing to make fun of for being utterly absurd, without substance and based on something deeply unscientific.
Then, after several months of intense meditation I started getting strong somatosensory perception in areas of my body traditionally associated with chakras, and Kundalini awakenings and the like. Terms I only picked up on after researching what might be happening.
In short, it strongly appears that if you take a group of people and have them perform certain practices for an extended period of time, you will create a relatively consistent cluster of symptoms.
Eastern mythology/religions have their own language to describe these phenomenona, and the alleged mechanisms are obviously ridiculous, but there is nevertheless something oddly consistent about reported experiences.
Thus, I think it's pretty sound to conclude that there is something "real" going on, creating a relatively consistent pattern of somatosensory experiences. The mechanism is almost certainly explainable by neuroscience but has received little serious exploration due to its purported mechanism and religious background.
> Now, that's not possible to prove scientifically yet
It may be that there is something to the idea that there are ways of stimulating certain parts of the body that can produce something like vagus nerve effects, but asserting it's true by the name given in an ancient mythology is a great way to derail any conversation.
0: https://www.amazon.in/Kundalini-untold-story-Om-Swami/dp/818... 1: https://news.ycombinator.com/item?id=6910041