The role of admixture in the rare variant contribution to inflammatory bowel disease

Astore, Courtney; Sharma, Shivam; Nagpal, Sini; Cutler, David J.; Rioux, John D.; Cho, Judy H.; McGovern, Dermot P. B.; Brant, Steven R.; Kugathasan, Subra; Jordan, I. King; Gibson, Greg

doi:10.1186/s13073-023-01244-w

Table 1 Allele frequencies and effects of rare coding variants affecting CD susceptibility

From: The role of admixture in the rare variant contribution to inflammatory bowel disease

Gene	rsID	Variant	AA MAF^d	EU MAF^d	Ratio^e	AA OR^f	EU OR^g	AA%VE	EU%VE	AA xs	EU xs
Rare variants associated with risk
HGFAC	rs16844401	R516H	0.028	0.070	0.40	1.25	1.17	0.27	0.32	13	19
SLC93A8	rs13107325	A391T	0.013	0.070	0.19	1.36	1.21	0.24	0.47	9	29
CCR7	rs2228015^a	M7V	0.007	0.038	0.18	1.17	1.15	0.03	0.14	2	10
DOK2	rs34215892^a	P274L	0.005	0.032	0.16	1.18	1.25	0.03	0.31	2	14
SDF2L1	rs73166641^a	R161H	0.006	0.013	0.46	2.30	1.24	0.83	0.12	15	7
NOD2	rs2066844^a	R702W	0.009	0.045	0.2	1.36	2.07	0.17	4.55	6	77
NOD2	rs2066845^a	G908R	0.003	0.015	0.2	1.96	2.34	0.27	2.14	6	36
NOD2	rs2066847^a	fs1007	0.003	0.023	0.13	2.03	3.00	0.30	5.42	6	79
NOD2	rs104895431^b	S431L	0.0004	0.0019	0.21	0.46	1.74	0.05	0.12	0	3
NOD2	rs104895438^c	A612T	0.0000	0.0002	n/a	n/a	3.12	n/a	0.05	0	1
NOD2	rs5743277^b	R703C	0.0008	0.0051	0.16	0.93	1.88	0.0008	0.40	1	9
NOD2	rs61747625^b	A755V	0.0007	0.0053	0.13	0.77	2.34	0.01	0.76	2	14
NOD2	rs104895443^c	E778K	0.0000	0.0004	n/a	n/a	3.03	n/a	0.10	0	2
NOD2	rs373550987^c	splice	0.0000	0.00006	n/a	n/a	4.97	n/a	0.03	0	1
NOD2	rs104895467^c	N852S	0.0001	0.0007	0.14	1.85	2.31	0.008	0.10	0	1
RELA	rs61759893^b	D291N	0.0011	0.006	0.18	0.69	1.46	0.03	0.17	1	5
PTAFR	rs138629813^b	N114S	0.0005	0.0038	0.13	0.93	1.70	0.0005	0.21	1	5
PDLIM5	rs182339387^b	splice	0.0007	0.004	0.18	0.93	1.61	0.0007	0.18	1	5
IL10RA	rs56143179^b	P295L	0.0001	0.0013	0.08	0.31	2.11	0.03	0.14	0	3
Rare variants associated with protection
IL23R	rs41313262^a	V362I	0.003	0.015	0.2	0.54	0.70	0.23	0.38	3	8
IL23R	rs11209026	R381Q	0.013	0.07	0.19	0.64	0.49	0.51	6.63	9	61
TYK2	rs35018800^b	A928V	0.001	0.008	0.13	2.32	0.60	0.14	0.41	1	6
TYK2	rs34536443^a	P1104A	0.009	0.044	0.21	1.22	0.72	0.07	0.91	0	21
TAGAP	rs41267765^a	E147K	0.006	0.022	0.27	0.81	0.79	0.05	0.24	2	9
CARD9	rs141992399^b	splice	0.001	0.006	0.17	n/a	0.47	n/a	0.68	0	6

Last two columns show the expected excess (xs) of cases per 100,000 individuals assuming prevalence 1%
VE Variance explained (VE)
^aRare variant (0.01 < EU MAF < 0.05); ^bVery rare variant (0.001 < EU MAF < 0.01); ^cUltra-rare variant (EU MAF ≤ 0.001)
^dMAF in this table refers to gnomAD African or Non-Finnish European frequencies
^eRatio of African American to European allele frequency in gnomAD
^fOdds ratios from AA-WGS cohort; not computed if MAF < 0.001
^gOdds ratios reported from Sazonovs meta-analysis

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ISSN: 1756-994X

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