"On what basis do Hindu philosophies say Atman exist?"
As per Bhagavad Gita, the supreme reality viz. Atman is said to be neither "existent" nor "non-existent".
BG 13.13 - I shall speak of that which is knowable (should be known). Knowing which, one attains immortality. The supreme Brahman dwelling under Me, is beginning-less. "That" is said to be neither existent nor non-existent.
"according to science it is gene only giving us a particular shape of a body."
Whatever our ancient scripts describe is actually a spiritual science (VignAna) itself.
I presume that you are referring to the modern Physics & Biology in this context. We should understand that they are ever-evolving. Whatever we knew 1000 year back, was changed 500 years back, which again changed 100 years back & so on. This is natural, because it depends on observation and inference.
There are people, who say that all the humanity came into existence primarily due to reproduction among male-female. Which is furthered into gene theory etc.
They don't believe in anything else due to short- sightedness. Such ignorant people are also described in Gita as of [partially or fully] demonic nature.
BG 16.8 - Without [any] truth, without [any] foundation, "they" call the universe with no Supreme; Without any mutuality, [it's] born from the purpose of what else but lust.