(covers information from several alternate timelines)
A phase variance was a term applicable to phenomena or technologies that show wave-like properties.
In 2368, on Devidia II, crew of the USS Enterprise-D devised a method of moving into the time continuum of the Devidians by phase-shifting to the positive phase variance of 0.004 percent. Data was enveloped in a contained subspace force field created by a subspace generator. By adjusting the synchronic distortion of the field with the phase discriminator in his positronic brain he phase-shifted himself. The procedure was repeated for other members of the crew using a tricorder modified to interface with the subspace generator, containing a custom built phase discrimination. It was theorized in both instances that the phase displacement was not precise enough to synchronize the Enterprise crew to the Devidians perceptual range, even though the Enterprise personnel could see them when phased. (TNG: "Time's Arrow")
In 2369, Reginald Barclay theorized that it may be possible to beam a holodeck object into the real world successfully if it could be locked on to, which would require compensating for the phase variance. He said this might be possible by modifying the pattern enhancers. (TNG: "Ship in a Bottle")
When attempting to transport Telek R'Mor through a micro-wormhole in 2371, the USS Voyager crew were hindered by a strange phase variance in the radiation stream, caused by the fact that the two ends of the wormhole were in separate time periods. (VOY: "Eye of the Needle")
Also in 2371, B'Elanna Torres reported a phase variance in plasma conduit 3 that she wanted to check out before engaging thrusters, in an attempt by Torres, Seska and Joe Carey to cover an illicit attempt to remain in the planets orbit to use a spatial trajector to shortcut 40,000 light years closer to the Alpha Quadrant. (VOY: "Prime Factors")
The interphase used by the Voth produce a localized spatial fluctuation with modulating phase variance. This allowed the Voyager crew to detect Forra Gegen and Tova Veer aboard their ship in 2373. (VOY: "Distant Origin")
In 2374, B'Elanna Torres determined that adjusting the sensors to a phase variance of 0.15 would allow them to detect the phased Srivani that had infiltrated Voyager. The Doctor later adjusted Seven of Nine's sensory nodes to do the same. (VOY: "Scientific Method")
Later that year, Torres speculated that a phase variance in the transporter was responsible for igniting a sample of protomatter that Neelix had attempted to collect from a class 1 nebula. (VOY: "Mortal Coil")
When Voyager constructed an experimental quantum slipstream drive in 2375, a 0.42 phase variance in the slipstream threshold emerged during testing, enough to overload the quantum matrix and force the starship out of slipstream with catastrophic results. After much discussion, Harry Kim proposed having the Delta Flyer stay ahead of Voyager, mapping the slipstream threshold as it forms and relaying phase corrections to dampen the variance.
During the initial flight, the phase variance emerged as in the tests. However, the phase corrections were unable to compensate for the rising phase variance, causing the failure of Voyager's helm controls and leaving the slipstream on the verge of collapse. Seven of Nine received a new set of phase corrections through her cranial implants that deactivated the drive. Along with the corrections was a message from a future Harry Kim in an alternate timeline.
In the older Kim's timeline, the phase variance caused the slipstream to collapse, throwing Voyager into normal space to crash on a Class L planet in the Takara sector, with the loss of all aboard. He had initially attempted, without success, to correct the phase variance so that Voyager could remain in the slipstream and return to the Alpha Quadrant, as he and Chakotay had in the Flyer – but when this failed, The Doctor, reactivated from Voyager's wreckage to assist in the attempt, convinced Kim to abandon this impossibility and "settle" for safely ending the ill-advised flight. (VOY: "Timeless")