Table 4 Filtered UCP3 gene variants after quality control check.

From: UCP3 gene variants and obesity in a Pakistani sample population

S. No.	Position	REF	ALT	Variant type	Allelic type	Alternate allele frequency		Alternate allele frequency in gnomAD (Total)	SAS alternate allele frequency gnomAD	ClinVar
S. No.	Position	REF	ALT	Variant type	Allelic type	Cases	Controls	Alternate allele frequency in gnomAD (Total)	SAS alternate allele frequency gnomAD	ClinVar
1	73711477	A	G	SNP	Biallelic	0.85	0.80	0.71	0.77*	NR
2	73711483	T	TG	Insertion	Multiallelic	0.75	0.71	0.51	0.57*	NR
3	73711483	T	TGG	Insertion	Multiallelic	0	0.14	0.003	0.02*	NR
4	73712020	A	G	SNP	Biallelic	0.72	0.74	0.60	0.51*	NR
5	73712708	G	GTC	Insertion	Biallelic	0.70	0.65	0.16	0.12*	Benign
6	73712720	CT	C	Deletion	Multiallelic	0.02	0	0.00001*	0*	NR
7	73712720	CT	CTCTT	Insertion	Multiallelic	0.04	0.01	0^*	0*	NR
8	73712720	CT	CTT	Insertion	Multiallelic	0.36	0.38	-	-	NR
9	73712720	CT	CTTT	Insertion	Multiallelic	0.08	0.11	-	-	NR
10	73712770	GA	GAA	Insertion	Biallelic	0.67	0.65	-	-	NR
11	73712824	C	T	SNP	Biallelic	0.50	0.50	0.003	0.02*	NR
12	73712859	T	C	SNP	Biallelic	0.72	0.76	0.66	0.56*	Benign
13	73713129	T	C	SNP	Biallelic	0.64	0.63	0.19	0.11*	NR
14	73713156	C	G	SNP	Multiallelic	0.66	0.57	0.27	0.21*	NR
15	73713156	C	T	SNP	Multiallelic	0.03	0.08	0.02	0.02*	NR
16	73713223	A	G	SNP	Biallelic	0.72	0.74	0.61	0.51*	NR
17	73713442	T	C	SNP	Biallelic	0.71	0.73	0.57	0.51*	NR
18	73713560	T	C	SNP	Biallelic	0.58	0.61	0.24	0.24*	NR
19	73713591	A	G	SNP	Biallelic	0.69	0.63	0.29	0.23*	NR
20	73713960	G	A	SNP	Biallelic	0.58	0.61	0.26	0.24*	NR
21	73714339	G	A	SNP	Biallelic	0.66	0.50	0.31	0.26*	Benign
22	73714562	G	A	SNP	Biallelic	0.58	0.61	0.26	0.24*	NR
23	73715115	T	G	SNP	Biallelic	0.50	0.55	0.02	0.04*	NR
24	73715134	C	T	SNP	Biallelic	0.67	0.60	0.10	0.09*	NR
25	73715542	G	A	SNP	Biallelic	0.73	0.71	0.57	0.52	Benign
26	73715666	G	A	SNP	Biallelic	0.79	0.71	0.26	0.23	Benign
27	73715707	G	T	SNP	Biallelic	0.63	0.50	0.002	0.005*	NR
28	73716101	T	C	SNP	Biallelic	0.55	0.69	0.002	0.02*	NR
29	73716277	G	A	SNP	Biallelic	0.67	0.69	0.39	0.29*	NR
30	73716469	A	G	SNP	Biallelic	0.62	0.61	0.30	0.26*	NR
31	73716530	G	A	SNP	Multiallelic	0	0.50	0.003	0.0006*	NR
32	73716530	G	C	SNP	Multiallelic	1.00	0	0.00003	0.002*	NR
33	73717024	A	T	SNP	Biallelic	0.70	0.69	0.52	0.47	Benign
34	73717025	T	C	SNP	Biallelic	0.70	0.70	0.52	0.47	Benign
35	73717074	G	A	SNP	Biallelic	0.58	0.62	0.24	0.23*	NR
36	73717121	C	T	SNP	Biallelic	0.58	0.63	0.26	0.24*	NR
37	73717254	A	G	SNP	Biallelic	0.60	0.64	0.29	0.26	Benign
38	73717567	C	G	SNP	Biallelic	0.68	0.68	0.64	0.49*	Benign
39	73718332	C	T	SNP	Biallelic	0.55	0.50	0.002	0.02*	NR
40	73718482	CTTT	C	Deletion	Multiallelic	0.01	0	0.00003*	0*	NR
41	73718482	CTTT	CTT	Deletion	Multiallelic	0.48	0.49	-	-	NR
42	73718482	CTTT	CTTTT	Insertion	Multiallelic	0.01	0.01	-	-	NR
43	73720165	G	A	SNP	Biallelic	0.55	0.57	0.24	0.23*	NR

Monomorphic variants were removed to retain only polymorphic sites. Singleton variants (appearing only once in the dataset) were excluded. Variants identified solely in the control subjects were eliminated, as they were considered non-disease-associated. Variant type, allelic type, alt. allele frequency of study population, total allele frequency of gnomAD, and SAS allele frequency gnomAD are given. Total and SAS alternate allele frquency reported by Variant Effect Predictor (VEP) but not present in the latest gnomAD database*. Dash (-) show absence of alternate allele frequency in VEP and gnomAD. Position = Chromosomal position (hg19) on chromosome 11. The alternate allele frequencies for the variants that are only present in cases are shown in bold. Abbreviations: REF, Reference allele; ALT, Alternate allele; SAS, South Asian population; NR, Not Reported in ClinVar; gnomAD, Genome Aggregation Database.

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Table 4 Filtered UCP3 gene variants after quality control check.

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