. 2023 May 18;14:1189976. doi: 10.3389/fphar.2023.1189976

TABLE 3.

Proposed non-exhaustive list and description of genetic allele variants for the clinical implementation of pharmacogenomics (PGx).

Gene	Allele	rsID	Variation type	Phenotype	MAF from 1,000 genomes with few exceptions ^a ^, ^b
Gene	Allele	rsID	Variation type	Phenotype	African	Asian	Europe
ABCG2	c.421	rs2231142	SNV	Decreased function	0.0129	0.2907	0.0944
CYP2B6	*9	rs3745274	SNV	Decreased function	0.3744	0.2153	0.2356
	*18	rs28399499	SNV	No function	0.0825	0.0000	0.0000
	*26	rs3826711	SNV	Decreased function	0.0000	0.0050	0.0000
CYP2C19	*2	rs12769205	SNV	No function	0.1967	0.3125	0.1451
		rs4244285	SNV		0.1702	0.3125	0.1451
		rs58973490	SNV		0.0008	0.0000	0.0040
	*3	rs4986893	SNV	No function	0.0023	0.0556	0.000
	*4	rs12248560	SNV	No function	0.2352	0.0149	0.2237
	*4	rs28399504	SNV	No function	0.0000	0.0010	0.0010
	*8	rs41291556	SNV	No function	0.0008	0.0000	0.0030
	*9	rs17884712	SNV	Decreased function	0.0098	0.0000	0.000
	*10	rs6413438	SNV	Decreased function	0.0015	0.0000	0.0000
	*17	rs12248560	SNV	Increased function	0.2352	0.0149	0.2237
CYP2C9	*2	rs1799853	SNV	Decreased function	0.0083	0.0010	0.1243
	*3	rs1057910	SNV	No function	0.0023	0.0337	0.0726
	*5	rs28371686	SNV	Decreased function	0.0166	0.0000	0.0000
	*6	rs9332131	Indel	No function	0.0083	0.0000	0.0000
	*8	rs7900194	SNV	Decreased function	0.0530	0.0000	0.0020
	*11	rs28371685	SNV	Decreased function	0.0242	0.0000	0.0020
	*13	rs72558187	SNV	No function	0.0000	0.0030	0.0000
	*14	rs72558189	SNV	Decreased function	0.0000	0.0010	0.0000
	*16	rs72558192	SNV	Decreased function	0.0000	0.0010	0.0000
	*29	rs182132442	SNV	Decreased function	0.0000	0.0030	0.0010
	*31	rs57505750	SNV	Decreased function	0.0015	0.0000	0.0000
	*33	rs200183364	SNV	No function	0.0000	0.0010	0.0000
	*45	rs199523631	SNV	No function	0.0000	0.0000	0.0010
CYP2D6	*3	rs35742686	Indel	No function	0.0040	0.0000	0.0189
	*4	rs3892097	SNV	No function	0.0605	0.0020	0.1859
		rs28371703	SNV		0.0204	0.0010	0.1730
		rs28371704	SNV		0.0204	0.0010	0.1730
		rs1058172	SNV		0.0000 ^a	0.0211 ^a	0.1125 ^a
	*5	PV00430	Whole gene deletion	No function	-	-	-
	*6	rs5030655	Indel	No function	0.0008	0.0000	0.0199
	*9	rs5030656	Indel	Decreased function	0.0008	0.0000	0.0258
	*10	rs1065852	SNV	Decreased function	0.1127	0.5714	0.2018
		rs1058164	SNV		0.6344 ^a	0.7230 ^a	0.5678 ^a
		rs1135840	SNV		0.6205 ^a	0.7180 ^a	0.5673 ^a
	*14	rs5030865	SNV	Decreased function	0.0000	0.0099	0.0000
	*17	rs28371706	SNV	Decreased function	0.2179	0.0000	0.0020
		rs1058164	SNV		0.6344 ^a	0.7230 ^a	0.5678 ^a
		rs16947	SNV		0.3398 ^a	0.0300 ^a	0.3181 ^a
		rs1135840	SNV		0.6205 ^a	0.7180 ^a	0.5673 ^a
	*21	rs1058164	SNV	No function	0.6344 ^a	0.7230 ^a	0.5678 ^a
		rs16947	SNV		0.3398 ^a	0.0300 ^a	0.3181 ^a
		rs1135840	SNV		0.6205 ^a	0.7180 ^a	0.5673 ^a
	*29	rs61736512	SNV	Decreased function	0.1097	0.0000	0.0000
	*29	rs59421388	SNV	Decreased function	0.1074	0.0000	0.0000
	*36	rs1065852	SNV	No function	0.1127	0.5714	0.2018
		rs1135822	SNV		0.0003 ^a	0.0180 ^a	0.0002 ^a
		rs1135823	SNV		0.0000	0.0000	0.0010
	*40	rs72549356	Indel	No function	0.0091	0.0000	0.0000
	*41	rs28371725	SNV	Decreased function	0.0182	0.0377	0.9066
	*xN	-	Copy number	Increased function	-	-	-
CYP3A5	*3	rs776746	SNV	No function	0.3035 ^a	0.7130 ^a	0.9299 ^a
	*6	rs10264272	SNV	No function	0.1543	0.0000	0.0030
	*7	rs41303343	Indel	No function	0.1180	0.0000	0.0000
CYP4F2	*3	rs2108622	SNV	Decreased function	0.0825	0.2143	0.2903
DPYD	*2A	rs3918290	SNV	Decreased function	0.0008	0.0000	0.0050
	*13	rs55886062	SNV	Decreased function	0.0000	0.0000	0.0010
	c.2846	rs67376798	SNV	Decreased function	0.0008	0.0000	0.0070
	c.1129-5923	rs75017182	SNV	Decreased function	0.0008	0.0000	0.0239
HLA-A	HLA-A*31:01	-	-	High-risk allele	-	0.0556	0.0104
HLA-B	HLA-B*15:02	-	-	High-risk allele	-	0.0667	-
	HLA-B*57:01	-	-	High-risk allele	-	0.0111	0.0729
	HLA-B*58:01	-	-	High-risk allele	0.0611	0.0444	0.0104
MT-RNR1	c.1555	rs267606617	SNV	Conformational change	-	0.0015 ^b	-
MT-RNR1	c.1095	rs267606618	SNV	-	-	0.0019 ^b	-
NUDT15	*2	rs746071566	Indel	No function	0.0015	0.0476	0.0030
NUDT15	*3	rs116855232	SNV	No function	0.0008	0.0952	0.0020
SLCO1B1	*5	rs4149056	SNV	No function	0.0136	0.1230	0.1610
	*9	rs59502379	SNV	No function	0.0408	0.0000	0.0000
	*14	rs11045819	SNV	Increased function	0.0598	0.0030	0.1441
	*15	rs2306283	SNV	No function	0.8177	0.7619	0.4026
TPMT	*2	rs1800462	SNV	No function	0.0008	0.0000	0.0060
	*3A	rs1800460	SNV	No function	0.0030	0.0000	0.0278
	*3A	rs1142345	SNV	No function	0.0666	0.0218	0.0288
	*3B	rs1800460	SNV	No function	0.0030	0.0000	0.0278
	*3C	rs1142345	SNV	No function	0.0666	0.0218	0.0288
UGT1A1	*6	rs4148323	SNV	Decreased function	0.0008	0.1379	0.0070
	*28	rs3064744	Indel: TA (8)	Decreased function	0.4266	0.1290	0.2922
	*36	rs3064744	Indel: TA (6)	Increased function	0.4266	0.1290	0.2922
	*37	rs3064744	Indel: TA (9)	Decreased function	0.4266	0.1290	0.2922
VKORC1	c. −1639	rs9923231	SNV	Decreased function	0.0545	0.8849	0.3877

MAF, minor allele frequency; SNV, single nucleotide variation; Indel, Insertion or Deletion.

^{^a}

From Alfa Allele Frequency.

^{^b}

From 14KJPN (Allele frequency panel of 14,129 Japanese individuals including the X chromosome).