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Withholding for unexpected Short-Term Capital Gains and Penalties
My understanding (I've never filed one myself) is that the 1040ES is intended to allow you to file quarterly and report unpredictable income, and to pay estimated taxes on that income.   I was in the same sort of boat for 2016 -- I had a big unexpected income source in 2015, and this took away my Safe Harbor for 2016.  I adjusted my w-2 to zero exemptions (eventually) and will be getting a refund of about 1% of our income. So lets say you make 10000 in STG in March, and another 15000 in STG in April.  File a quarterly 1040-ES between March 31 and April 15.  Report the income, and pay some tax.  You should be able to calculate the STCG Tax for 10k pretty easily.  Just assume that it comes off the top and doesn't add at all to your deductions.  Then for April, do the same by June 15. Just like your W-2 is used to estimate how much your employer should withhold, the 1040ES is designed to estimate how much extra you need to pay to the IRS to avoid penalties.  It'll all get resolved after you file your final 1040 for the 2017 calendar year.