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To delete a taxonomy term, deleteTaxonomyTerm mutation should be used.
Important: this operation is irreversible. After the term deletion, it will disappear from all content items where it was used.
Access policy:
  • The API user context should have permission to update the given taxonomy term.
  • A term with the given ID should exist on the site.
The only argument that is used in the mutation is termId (required). Now let’s delete the term that was created before (see Create a taxonomy term for more details). 
mutation deleteTaxonomyTerm {
  deleteTaxonomyTerm(termId: "11") {
    errors
    response
  }
}
After the mutation execution the term was deleted: After term deletion
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