Clear quartz has the largest role of any stone in modern crystal practice and one of the smallest documented roles in any ancient one, and the gap between those two facts is the most interesting thing about it.
Rock crystal was certainly used in antiquity. It was carved into vessels, lenses and seals; the Greek krystallos means ice, reflecting a belief recorded by Pliny that quartz was water frozen so hard it could not thaw; and crystal spheres and lenses appear in Roman, Sasanian and later European contexts. Agrippa pairs rock crystal with the fixed star Alcyone in the Behenian list. Scrying with a crystal ball is documented in early modern Europe, and John Dee's shewstones survive.
What is not documented is the modern framework: quartz as a programmable master crystal, amplifying and storing intention, cleansed and charged by moonlight or salt, working with all chakras, arranged in grids. That framework is twentieth century. Its components arrive from several directions, Theosophy, the chakra literature as westernised from the late nineteenth century, and above all the metaphysical publishing boom from the 1970s and 1980s, in which quartz's genuine electronic role was borrowed as a metaphor and then treated as a mechanism.
The claim that Atlantean or Lemurian civilisations used quartz technology, and the associated categories of record-keeper and Lemurian seed crystals, originate in that same period and have no antecedent.
None of this makes the practice illegitimate as a practice. It makes the standard claim of ancient provenance false, and that claim is made constantly. A tradition that is fifty years old is worth describing accurately as fifty years old.