The decision, which enables Medicare reimbursement, is effective for tests administered on or after Dec. 1.
Starting in late 2020, public health insurance is expected to pay for NIPT if a trisomy is suspected and this constitutes an "unacceptable burden" for the pregnant woman.
The government payor asked the public to specifically weigh in on the evidence supporting germline testing to assess treatment benefit for patients with hereditary cancer syndromes.
CMS had received significant stakeholder feedback that germline NGS testing is not the same as somatic testing, and that the NCD as written would negatively impact patients.
The agency said it is sensitive to stakeholder concerns and is working with MACs to adjust claims processing systems.
The test is designed to analyze a panel of 112 genes to help in the diagnosis of thyroid nodules with indeterminate fine-needle aspiration cytology.
An Oregon Health Authority committee issued a draft guidance to not cover NGS testing for solid tumors, which advocacy groups say will limit access to Medicaid beneficiaries.
The move is precipitated by CMS's decision to grant national coverage to NGS companion diagnostics when they're approved by the FDA.
A private payor survey by ClearView Healthcare Partners found that medical directors viewed CMS's decision with caution; half had no plans to align commercial plan coverage.
The policy states that lab tests without FDA's blessing may pursue local coverage via Medicare contractors, but national coverage requires premarket approval or clearance.