With $40,631 SSA-1099 Box 5 + $12,000 IRA distribution + $3,847 interest = $56,478, why is only $6339 of social security taxable? I have $16,617 in deductions

Up to 85% of Social Security becomes taxable when all your other income plus 1/2 your social security, reaches:

Married Filing Jointly: $32,000

Single or head of household: $25,000

Married Filing Separately: 0

To see the Social Security Benefits Calculation Worksheet  in Turbo Tax Online version you would have to save your return with all the worksheets to your computer.   Or if you are using the Desktop CD/Download Software you can switch to Forms Mode (click Forms in the upper right) and click on SS in the list on the left side.

Is your Social Security taxable?

https://ttlc.intuit.com/community/income/help/is-my-social-security-income-taxable/00/25600

IRS Pub. 915 on Social Security.  There is a blank worksheet on page 16

https://www.irs.gov/pub/irs-pdf/p915.pdf

Up to 85% of Social Security Retirement/Disability/Survivors benefits becomes taxable when all your other income plus 1/2 your social security reaches:

• Married Filing Jointly - $32,000
• Single or Head of Household - $25,000
• Married Filing Separately - 0