Clean, Low-Emission, Affordable, New Transportation Efficiency Act

Clean, Low-Emission, Affordable, New Transportation Efficiency Act - Establishes the Low Greenhouse Gas Transportation Fund.

Requires the Administrator of the Environmental Protection Agency (EPA), for each of calendar 2012-2050, to auction 10% of emission allowances established under any EPA program providing for the reduction of greenhouse gas emissions and the auctioning of emission allowances.

Requires deposit of auction proceeds into the Fund to implement state and eligible regional or local entity greenhouse gas emission reduction plans, and provide funding to transit projects that help reduce such emissions.

Requires states and eligible regional or local entities representing populations of more than 200,000 people to: (1) establish goals for reducing greenhouse gas emissions from the transportation sector for the next 10 years; and (2) develop transportation greenhouse gas emission reduction plans, including supporting lists of prioritized transit projects, that are integrated into state and eligible regional or local entity long-range transportation and transportation improvement plans.

Directs the Secretary of Transportation and the EPA Administrator to contract with the Transportation Research Board of the National Academy of Sciences to study and report recommendations for improving research tools and federal data sources necessary to assess the effect of state and local transportation, land use, and environmental plans on motor vehicle use rates and transportation sector greenhouse gas emissions.