Table 2.

Table of variant–specific summaries: variant name (columns 1 and 5), prior classification (columns 2 and 6), posterior probability that the variant is protein damaging (columns 3 and 7); and natural logarithm of the posterior odds in favor of the variant being protein damaging (columns 4 and 8)

VariantClassificationPosterior probability damagingloge posterior oddsaVariantClassificationPosterior probability damagingloge posterior oddsa
5673insCPathogenicb1.0000M1783LVUS0.0013−6.63
del17/18Pathogenic1.0000M1783TVUS0.0346−3.33
W1837XPathogenic1.0000P1614SVUS0.00010.0011−6.82
WTNeutralc0.0000P1771LVUS0.0066−5.01
Y1853XPathogenic1.0000P1806AVUS0.0016−6.45
A1669SVUS0.0625−2.71P1812AVUS0.0050−5.29
A1708EVUS1.000017.67P1859RVUS0.00010.0013−6.64
A1752PVUS1.000018.02Q1785HVUS0.0012−6.77
A1823TVUS0.99998.89Q1826HVUS0.0031−5.77
A1830TVUS0.0015−6.53R1443GVUS0.0223−3.78
C1697RVUS0.99999.50R1495MVUS0.0019−6.24
D1546NVUS0.0015−6.51R1699LVUS1.000017.50
D1692NVUS0.0948−2.26R1699QVUS0.99876.65
E1644GVUS0.0016−6.45R1699WVUS0.87951.99
E1794DVUS0.0013−6.62R1726GVUS0.0013−6.66
F1662SVUS0.0001d0.0017−6.40R1751PVUS1.000017.54
F1695LVUS0.0013−6.63R1751QVUS0.00010.0022−6.11
G1706AVUS1.000011.85R1753TVUS1.000017.57
G1706EVUS0.999e1.000016.61R1835QVUS0.0021−6.15
G1738EVUS0.99525.34S1512IVUS0.00010.0013−6.62
G1738RVUS0.99f1.000017.39S1613CVUS0.0012−6.69
G1788DVUS0.0147−4.21S1613GVUS0.00010.0009−7.03
G1788VVUS1.000017.80S1655FVUS0.99957.56
H1402YVUS0.0032−5.73S1715NVUS0.99947.49
H1421YVUS0.0017−6.37S1715RVUS0.99978.16
H1746NVUS0.0231−3.74T1685IVUS0.991.000018.59
I1766SVUS1.000016.01T1700AVUS0.4291−0.29
K1487RVUS0.0045−5.39T1720AVUS0.00010.0014−6.59
K1847RVUS0.0025−5.98V1534MVUS0.00010.0011−6.81
L1407PVUS0.4052−0.38V1665MVUS0.0263−3.61
L1564PVUS0.0058−5.14V1688delVUS0.990.99957.60
L1664PVUS0.0017−6.38V1713AVUS1.000014.52
L1764PVUS0.991.000016.85V1736AVUS0.99988.69
L1844RVUS0.0013−6.62V1741GVUS0.78911.32
M1628TVUS0.0031−5.77V1804DVUS0.00010.0057−5.17
M1628VVUS0.0031−5.78V1809FVUS1.000017.74
M1628V+S1613GVUS0.0026−5.97V1833MVUS0.0017−6.36
M1652IVUS0.0013−6.63W1837RVUS1.000016.96
M1689RVUS1.000016.00WTdelta14VUS0.0013−6.67
M1775KVUS1.000013.37WTdelta14+S1616GVUS0.0012−6.74
M1775RVUS0.991.000017.24
  • aThe posterior odds are equivalent to the Bayes factor, Embedded Image, because the prior distribution is uniform, and could be combined in this form with other conditionally independent data types.

  • bKnown pathogenic variant (“negative control”).

  • cWild–type, known benign variant (“positive control”).

  • dVariant of unknown significance (VUS) previously classified as neutral with an estimated posterior probability of pathogenicity less than 0.0001 but blinded for purposes of model evaluation.

  • eVUS previously classified as pathogenic with an estimated posterior probability greater than 0.999 but blinded for purposes of model evaluation.

  • fVUS previously classified as pathogenic with an estimated posterior probability of between 0.99 and 0.999 but blinded for purposes of model evaluation.