A new BART tunnel beneath the bay might begin in Alameda and emerge in Mission Bay. It could parallel the existing tube but then head up Mission Street on the west side of the bay instead of up Market. Or maybe it would stretch between Alameda and AT&T Park.

No one knows, but after years of supposition and pie-in-the-sky conjecture from planners and passengers alike, BART officials are starting to study a second Transbay Tube.

It would be the biggest Bay Area infrastructure project, probably, since the BART system was built more than 50 years ago, and it would cost twice as much as the new Bay Bridge, from $12 billion to $15 billion at a minimum.

“It’s going to be a huge investment. This cross-bay connection and its alignment are going to be very important,” said Jim Wunderman, CEO of the Bay Area Council, a business advocacy group that is active in transportation issues.

“Since we’re at the beginning, we need to look at the big picture,” he said. “We need to make sure we do it in a way that we don’t look back and say we should have done this differently.”

Much of the talk about a new rail tunnel has centered on its location, or alignment, including where the BART lines would head once they emerge from the tube, and how they could connect with jobs and housing.

“It’s less about the tube or getting across the water. It’s about the connections on either side ,” said Randy Rentschler, a spokesman for the Metropolitan Transportation Commission.

In a presentation to BART directors at a recent workshop, Ellen Smith, BART’s strategic planning manager, said it will be important to speak with San Francisco, Oakland and Alameda County officials about housing and jobs plans before analyzing alignments.

New BART lines connecting to the second tube could serve emerging neighborhoods and employment centers as well as areas now distant from stations, Rentschler said. Another tube would also mean that if BART were forced to shut down one tunnel for an emergency or repairs, the other would be available, Wunderman said. Today, a Transbay Tube shutdown paralyzes the system.

But other issues would also need to be studied, Smith said.

Those include everything from the cost; who would pay for it and how; and whether it would also carry high-speed rail or commuter trains like Caltrain and the Capitol Corridor. Those rail services operate on narrower tracks than BART does, so a new transbay tunnel would have to include separate tracks to accommodate both.

The Capitol Corridor, which operates between Sacramento and San Jose, could use the tube to provide a direct link to San Francisco instead of requiring passengers to transfer to a bus in Emeryville or BART in Richmond.

“It would be a complete game changer for us to have a one-seat ride all the way from Sacramento into San Francisco and all the connections available there,” said David Kutrosky, managing director of the Capitol Corridor, which is managed by BART. “We want to be part of this study.”

Caltrain and California High-Speed Rail, both of which are expected to eventually reach the Transbay Transit Center in South of Market, have also been mentioned as possible users of a future rail tunnel beneath the bay. Amtrak lines could also use the tunnel.

All of those services could be tapped to help pay for the new rail tunnel if it gets built, although taxpayers would undoubtedly also pay. BART officials say the cost of similar tunnel projects around the country, including the proposed Gateway rail tunnels beneath the Hudson River in New York and New Jersey, fall in the estimated cost range pegged to the second transbay tube. Gateway is estimated at $13 billion.

BART plans to pay for a variety of studies and some early engineering with some of the $200 million set aside in Measure RR, its $3.5 billion system modernization bond. Regional Measure 3, the Bay Area toll increase proposal on the June ballot, would set aside $50 million to further study the new tube, and Caltrans and the state Transportation Agency have said study money should be available as well, Kutrosky said.

Transportation and planning experts agree BART shouldn’t rush to commit to a new bay tunnel without thorough research, but they also caution that BART shouldn’t take too long to decide.

BART’s new fleet of rail cars and a new control system that allows trains to run closer together are expected to increase the capacity of the existing Transbay Tube — which currently carries as many trains as it can during peak hours — by as much as 25 percent by about 2025.

But by 2030, the tube will be at capacity again, said Tamar Allen, BART’s chief maintenance and engineering officer, meaning a new tube would be needed to keep up with anticipated regional and ridership growth. So BART officials are tentatively aiming for that year to have a new tube in service.

BART General Manager Grace Crunican said that given the amount of work that needs to be done, 12 years is not much time.

“If we’re talking about a second tube,” she said, “that’s tomorrow.”

Michael Cabanatuan is a San Francisco Chronicle staff writer. Email: mcabanatuan@sfchronicle.com Twitter: @ctuan

By the numbers

$12 billion Estimated minimum cost for a second BART tunnel under the bay

25% Increase in capacity in the current Transbay Tube expected by 2025 due to new, improved equipment

$200 million Amount BART has set aside from Measure RR for study and early engineering of a new tunnel

2030 The year that capacity is again expected to be reached in the current tunnel