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).

Variant	Classification	Posterior Probability Damaging	loge Posterior Odds⋄	Variant	Classification	Posterior Probability Damaging	loge Posterior Odds⋄
5673insC	Pathogenic†	1.0000		M1783L	VUS	0.0013	-6.63
del17/18	Pathogenic	1.0000		M1783T	VUS	0.0346	-3.33
W1837X	Pathogenic	1.0000		P1614S	VUS0.0001	0.0011	-6.82
WT	Neutral‡	0.0000		P1771L	VUS	0.0066	-5.01
Y1853X	Pathogenic	1.0000		P1806A	VUS	0.0016	-6.45
A1669S	VUS	0.0625	-2.71	P1812A	VUS	0.0050	-5.29
A1708E	VUS	1.0000	17.67	P1859R	VUS0.0001	0.0013	-6.64
A1752P	VUS	1.0000	18.02	Q1785H	VUS	0.0012	-6.77
A1823T	VUS	0.9999	8.89	Q1826H	VUS	0.0031	-5.77
A1830T	VUS	0.0015	-6.53	R1443G	VUS	0.0223	-3.78
C1697R	VUS	0.9999	9.50	R1495M	VUS	0.0019	-6.24
D1546N	VUS	0.0015	-6.51	R1699L	VUS	1.0000	17.50
D1692N	VUS	0.0948	-2.26	R1699Q	VUS	0.9987	6.65
E1644G	VUS	0.0016	-6.45	R1699W	VUS	0.8795	1.99
E1794D	VUS	0.0013	-6.62	R1726G	VUS	0.0013	-6.66
F1662S	VUS0.0001*	0.0017	-6.40	R1751P	VUS	1.0000	17.54
F1695L	VUS	0.0013	-6.63	R1751Q	VUS0.0001	0.0022	-6.11
G1706A	VUS	1.0000	11.85	R1753T	VUS	1.0000	17.57
G1706E	VUS0.999○	1.0000	16.61	R1835Q	VUS	0.0021	-6.15
G1738E	VUS	0.9952	5.34	S1512I	VUS0.0001	0.0013	-6.62
G1738R	VUS0.99●	1.0000	17.39	S1613C	VUS	0.0012	-6.69
G1788D	VUS	0.0147	-4.21	S1613G	VUS0.0001	0.0009	-7.03
G1788V	VUS	1.0000	17.80	S1655F	VUS	0.9995	7.56
H1402Y	VUS	0.0032	-5.73	S1715N	VUS	0.9994	7.49
H1421Y	VUS	0.0017	-6.37	S1715R	VUS	0.9997	8.16
H1746N	VUS	0.0231	-3.74	T1685I	VUS0.99	1.0000	18.59
I1766S	VUS	1.0000	16.01	T1700A	VUS	0.4291	-0.29
K1487R	VUS	0.0045	-5.39	T1720A	VUS0.0001	0.0014	-6.59
K1847R	VUS	0.0025	-5.98	V1534M	VUS0.0001	0.0011	-6.81
L1407P	VUS	0.4052	-0.38	V1665M	VUS	0.0263	-3.61
L1564P	VUS	0.0058	-5.14	V1688del	VUS0.99	0.9995	7.60
L1664P	VUS	0.0017	-6.38	V1713A	VUS	1.0000	14.52
L1764P	VUS0.99	1.0000	16.85	V1736A	VUS	0.9998	8.69
L1844R	VUS	0.0013	-6.62	V1741G	VUS	0.7891	1.32
M1628T	VUS	0.0031	-5.77	V1804D	VUS0.0001	0.0057	-5.17
M1628V	VUS	0.0031	-5.78	V1809F	VUS	1.0000	17.74
M1628V+S1613G	VUS	0.0026	-5.97	V1833M	VUS	0.0017	-6.36
M1652I	VUS	0.0013	-6.63	W1837R	VUS	1.0000	16.96
M1689R	VUS	1.0000	16.00	WTdelta14	VUS	0.0013	-6.67
M1775K	VUS	1.0000	13.37	WTdelta14+S1616G	VUS	0.0012	-6.74
M1775R	VUS0.99	1.0000	17.24

^⋄The posterior odds are equivalent to the Bayes Factor, Pr(Data ∣ Damaging)/Pr(Data ∣ Benign), because the prior distribution is uniform, and could be combined in this form with other conditionally independent data types.

^†Known pathogenic variant (“negative control”).

^‡Wild–type, known benign variant (“positive control”).

^*Variant 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.

^○VUS previously classified as pathogenic with an estimated posterior probability greater than 0.999, but blinded for purposes of model evaluation.

^●VUS previously classified as pathogenic with an estimated posterior probability of between 0.99 and 0.999, but blinded for purposes of model evaluation.