Prioritising positively selected variants in whole-genome sequencing data using FineMAV

Wahyudi, Fadilla; Aghakhanian, Farhang; Rahman, Sadequr; Teo, Yik-Ying; Szpak, Michał; Dhaliwal, Jasbir; Ayub, Qasim

doi:10.1186/s12859-021-04506-9

BMC Bioinformatics

Table 3 Top 10 FineMAV candidates from the Han Chinese (90HC), Singaporean Indian (SSIP) and Singaporean Malay (SSMP) populations

From: Prioritising positively selected variants in whole-genome sequencing data using FineMAV

Chr	Position ^a	SNP ID	Gene	Consequence ^b	DAF 90HC	DAF SSIP	DAF SSMP	FineMAV	Known or novel
90HC
2	109513601	rs3827760:A > G	EDAR	Missense (p.Val370Ala)	0.922	0.029	0.490	4.661	Known [3, 17, 18]
5	176099727	rs13186794:A > G	–	Intergenic	0.494	0.057	0.047	4.114	Novel
5	176099728	rs13186795:A > G	–	Intergenic	0.494	0.057	0.057	4.096	Novel
4	31442427	rs56345433:G > A	–	Intergenic	0.528	0.086	0.021	3.211	Novel
3	98031307	rs2316271:T > A	OR5H8	Stop gained (p.Leu184Ter)	0.767	0.314	0.599	3.102	Novel
16	31088347	rs749671:G > A	ZNF646	Synonymous (p.Glu234 =)	0.906	0.043	0.776	3.053	Known [18]
5	76129053	rs631465:T > C	F2RL1	Synonymous (p.Ile207 =)	0.522	0.014	0.208	3.008	Novel
2	109451118	rs72627476:A > G	CCDC138	Intronic	0.917	0.029	0.484	2.961	Known [3]
12	132106717	rs10794470:T > C	AC117500.3	Intronic	0.272	0.000	0.005	2.940	Novel
7	14587199	rs10236893:G > A	DGKB	Intronic	0.417	0.029	0.120	2.895	Novel
SSIP
16	28506428	rs151233:C > T	APOBR	Synonymous (p.Leu22 =)	0.006	0.571	0.026	7.677	Novel
16	30936081	rs35675346:G > A	FBXL19	Missense (p.Glu10Lys)	0.061	0.800	0.188	7.213	Known [18, 43]
16	28505660	rs151234:G > C	CLN3	Intronic	0.006	0.571	0.031	6.839	Novel
16	31044683	rs58726213:A > G	STX4	Upstream gene	0.089	0.871	0.214	6.686	Known [18, 43]
15	64592833	rs114713921:T > C	CSNK1G1	5 prime UTR	0.006	0.486	0.036	6.341	Novel
16	30666367	rs3747481:C > T	PRR14	Missense (p.Pro359Leu)	0.100	0.857	0.245	6.090	Known [18]
19	49206674	rs601338:G > A	FUT2	Stop gained (p.Trp154Ter)	0.011	0.186	0.016	6.033	Known [44]
15	91452595	rs2106673:A > G	MAN2A2	Missense (p.Gln412Arg)	0.017	0.514	0.063	5.746	Novel
10	17407147	rs729170:G > T	ST8SIA6	Intronic	0.006	0.343	0.005	5.736	Novel
15	64653984	rs8026043:G > T	PCLAF	Downstream gene	0.006	0.486	0.036	5.726	Novel
SSMP
2	98272491	rs2290123:A > G	ACTR1B	3 prime UTR	0.033	0.029	0.380	3.378	Known [18]
2	97613974	rs114979404:C > G	FAM178B	Intronic	0.022	0.029	0.375	2.806	Known [18]
17	2238152	rs79597880:T > C	TSR1	Missense (p.Lys199Glu)	0.089	0.014	0.297	2.747	Novel
16	31088347	rs749671:G > A	ZNF646	Synonymous (p.Glu234 =)	0.906	0.043	0.776	2.616	Known [18]
7	100371358	rs2293766:G > A	ZAN	Stop gained (p.Trp1883Ter)	0.528	0.257	0.557	2.531	Known [3, 45]
2	109513601	rs3827760:A > G	EDAR	Missense (p.Val370Ala)	0.922	0.029	0.490	2.474	Known [3, 17, 18]
3	98031307	rs2316271:T > A	OR5H8	Stop gained (p.Leu184Ter)	0.767	0.314	0.599	2.424	Novel
11	62848487	rs11231341:A > C	SLC22A24	Stop gained (p.Tyr501Ter)	0.867	0.757	0.792	2.421	Novel
12	57865558	rs2229300:G > T	GLI1	Missense (p.Gly1012Val)	0.050	0.014	0.224	2.402	Novel
16	31075175	rs2303223:G > A	ZNF668	Synonymous (p.Gly225 =)	0.911	0.043	0.781	2.290	Known [3]

^aThe genomic position according to the GRCh37/hg19 reference genome
^bThe most severe variant consequence according to Ensembl
Chr: chromosome, DAF: derived allele frequency, UTR: untranslated region

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ISSN: 1471-2105

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