The Land and Building Transaction Tax (LBTT) is set to be introduced next April but its rates have yet to be disclosed, and "there would be clear winners and losers depending on the scenario selected by Scottish Government", say accountants PwC.
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Susannah Simpson, tax partner at PwC in Scotland, said: "The shift from the existing slab tax system to a more progressive regime could potentially result in around 50 to 70 per cent of house buyers being exempt from paying LBTT. This would be hugely beneficial for first-time buyers and those on low incomes."
The present stamp duty is a one per cent 'slab' rate on properties up to £250,000, then 3 per cent. The LBTT has two possible scenarios: 7.5 per cent on properties above £180,000, or 2 per cent above £125,000 and up to £250,000, then 9.5 per cent above £250,000.
PwC says the average Scottish home will cost £198,000 next year, triggering £1,980 in stamp duty. Under LBTT the bill would come down to £1,350 or £1,460, saving £630 or £520. But on a £300,000 property, LBTT would be roughly the same as stamp duty at £9,000 under scenario one, but under the second scenario the bill would fall to £7,250.
Ms Simpson said: "It's clear that there could be significant variations in property taxes. If we are to get the property market moving on an upward trajectory, it's vital that people understand sooner rather than later what the impact on their pocket could be."
Meanwhile, a survey by Nationwide suggests Glasgow homebuyers are paying an average premium of £9,400 for a property within 500 yards of a rail station compared with one 1500m away.
The building society's research found 72 per cent of properties in Greater Glasgow are within one mile of a railway or Subway station, rising to over 80 per cent in Glasgow City, Inverclyde and West Dunbartonshire. Around 113m passenger journeys were made from Strathclyde's 175 railway and 15 Subway stations in 2012-13.
Robert Gardner, Nationwide's chief economist, said: "Glasgow has the largest network of suburban railway lines in the UK outside of London. We examined how the proximity to a railway or Subway station impacted property prices in the SPT area, after taking account of other property characteristics, such as property type, size and local neighbourhood type.
"Our research suggests that people are willing to pay a modest premium to be close to a station."
A property located 1,000 yards from a station commands a 2.6 per cent premium, at 75 yards it increases to 4.2 per cent, and for a property within 500 yards the premium is 6 per cent, or £9,400 on the average sale.
In Glasgow City, 60 per cent of properties are within 500 yards a station.
Mr Gardner said: "While those living in and around Glasgow clearly place a value on proximity to rail links, the evidence suggests that they aren't willing to pay as much extra to be near them as those in London or Greater Manchester.
"In the (UK) capital, this probably reflects a greater reliance on public transport, with residents less likely to drive to and from work."
House price growth is stronger in Scotland than most regions of the UK, according to figures out this week, and the average first-time deposit is lower.
UK house prices increased by 10.2 per cent in the year to June 2014, inflated by the boom in London (up 19.3 per cent) and the South-East. But while prices fell in seven English and Welsh regions, they rose by 6 per cent in Scotland, the Office of National Statistics said. First-time buyer deposits however were lower in Scotland, at an average £15,005, in July than in any other UK region except the north-east (where the average is only £10,170), according to the latest index from LSL, the Your Move estate agency group.
David Newnes, director of LSL, commented: "Outside of the (UK) capital, Help to Buy is giving many households a much-needed leg up onto the ladder."
Homes for Scotland, the builders' group, said Help to Buy (Scotland) had generated over 4,300 sales and reservations since launch less than a year ago - but the money had run out too soon.
Chief executive Philip Hogg said: "The impact is already apparent with significant drops in sales in the weeks since the budget expired in July. We therefore fear a return to decline in the months ahead. The high level of interest in the scheme was immediately apparent from launch and we have therefore consistently called for additional budget, or for future budget to be brought forward, to ensure the demand which clearly exists can be met."