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Table 5 Comparison of A3D, A3F, A3G and A3H allele frequencies between our South African population (SA) and other African populations in the 1000 Genome Project including: the African Caribbeans in Barbados (ACB), Americans of African Ancestry in USA (ASW), Esan in Nigeria (ESN), Gambian in the Western Gambia (GWD), Luhya in Webuye, Kenya (LWK), Mende in Sierra Leone (MSL) and Yoruba in Ibadan, Nigeria (YRI)

From: Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa

Amino acid change and variant ID Allele (2n) SA (336) ACB (192) ASW (122) ESN (198) GWD (226) LWK (198) MSL (170) YRI (216)
APOBEC 3D nonsynonymous allele frequencies (%)
R6K (NI) G (R) A (K) 94.9 5.1 NI NI NI NI NI NI NI
R97C (rs75858538) C (R) T (C) 93.8 6.2 97 3 (P = 0.1506) 94 6 (P = 1.0) 97 3 (P = 0.0614) 98 2 (P = 0.0253)* 94 6 (P = 1.0) 98 2 (P = 0.0262)* 97 3 (P = 0.1631)
L221R (NI) T (L) G (R) 99.1 0.9 NI NI NI NI NI NI NI
C224Y (rs772893975) G (C) A (Y) 97.9 2.1 ND ND ND ND ND ND ND
T238A (rs201709403) A (T) G (A) 95.8 4.2 100 0 (P = 0.0030)* 99 1 (P = 0.1322) 100 0 (P = 0.0016)* 100 0 (P = 0.0012)* 100 0 (P = 0.0016)* 100 0 (P = 0.0036)* 100 0 (P = 0.0013)*
T238I (NI) C (T) T (I) 97.6 2.4 NI NI NI NI NI NI NI
R248K (rs61748819) G (R) A (K) 89.0 11.0 91 9 (P = 0.4596) 96 4 (P = 0.0267)* 86 14 (P = 0.3375) 92 8 (P = 0.3890) 87 13 (P = 0.5785) 86 14 (P = 0.4668) 87 13 (P = 0.5018)
C320Y (rs61999542) G (C) A (Y) 99.7 0.3 ND ND ND ND ND ND ND
APOBEC3D synonymous allele frequencies (%)
L221 L (rs769426665) G (L) C (L) 99.1 0.9 ND ND ND ND ND ND ND
T316 T (rs184448269) C (T) T (T) 97.9 2.1 99 1 (P = 0.3657) 99 1 (P = 0.3657) 98 2 (P = 0.3657) 99 1 (P = 0.3657) 99 1 (P = 0.3657) 98 2 (P = 0.3657) 99 1 (P = 0.3657)
APOBEC 3F nonsynonymous allele frequencies (%)
R48P (rs35053197) G (R) C (P) 96.1 3.9 98 2 (P = 0.3074) 98 2 (P = 0.3670) 95 5 (P = 0.8202) 99 1 (P = 0.1100) 95 5 (P = 0.6559) 98 2 (P = 0.2763) 95 5 (P = 0.6663)
A78V (rs5750728) C (A) T (V) 79.9 20.1 78 22 (P = 0.6518) 73 27 (P = 0.1236) 82 18 (P = 0.6453) 77 23 (P = 0.3943) 76 24 (0.3756) 85 15 (P = 0.2183) 86 14 (P = 0.0798)
I87L (rs146543452) A (I) C (L) 99.7 0.3 100 0 (P = 1) 100 0 (P = 1) 100 0 (P = 1) 98 2 (P = 0.0878) 99 1 (P = 1) 99 1 (P = 1) 100 0 (P = 1)
Q87L (rs114704208) A (Q) T (L) 97.1 2.9 92.2 7.8 (P = 0.0171)* 93.4 6.6 (P = 0.0994) 96.5 3.5 (P = 0.7961) 96.0 4.0 (P = 0.6287) 93.0 7.0 (P = 0.0718) 94.7 5.3 (P = 2141) 94.4 5.6 (P = 0.1738)
A108S (rs2020390) G (A) T (S) 62.3 37.7 67 33 (P = 0.2922) 66 34 (P = 0.5796) 69 31 (P = 0.1268) 62 38 (P = 0.8572) 65 35 (P = 0.6371) 76 24 (P = 0.0031)* 70 30 (P = 0.0619)
V231I (rs2076101) G (V) A (I) 89.0 11.0 79 21 (P = 0.0041)* 73 27 (P = 0.0001)* 84 16 (P = 0.1053) 78 22 (P = 0.0007)* 80 20 (P = 0.0092)* 85 15 (P = 0.2485) 87 13 (P = 0.5829)
Y307C (rs12157816) A (Y) G (C) 95.1 4.9 95 5 (P = 0.8368) 98 2 (P = 0.1703) 96 4 (P = 0.5129) 98 2 (P = 0.1649) 98 2 (P = 0.1489) 96 4 (P = 0.8218) 95 5(P = 1.0)
APOBEC3F synonymous allele frequencies (%)
I117I (NI) C (I) T (I) 99.4 0.6 NI NI NI NI NI NI NI
S118S (rs35928287) C (S) T (S) 86.7 13.3 ND ND ND ND ND ND ND
R143R (rs4821862) C (R) T (R) 41.9 58.1 45 55 (P = 0.5775) 45 55 (P = 5892) 39 61 (P = 0.6433) 50 50 (P = 0.0794) 45 55 (P = 0.4624) 46 54 (P = 0.3372) 47 53 (P = 0.2840)
Y196Y (rs765418322) T (Y) C (Y) 89.6 10.4 ND ND ND ND ND ND ND
S229S (rs549550231) A (S) G (S) 99.4 0.6 ND ND ND ND ND ND ND
E245E (rs113109079) G (E) A (E) 97.1 2.9 99 1 (P = 0.2175) 98 2 (P = 0.7356) 100 0 (P = 0.0139)* 98 2 (P = 0.5717) 99 1 (P = 0.0971) 98 2 (P = 0.5517) 98 2 (P = 0.1350)
S327S (rs35895636) C (S) T (S) 90.6 9.4 98 2 (P = 0.0013)* 99 1 (P = 0.0006)* 96 4 (P = 0.0126)* 100 0 (P = 0.0001)* 97 3 (P = 0.0064)* 100 0 (P = 0.0001)* 98 2 (P = 0.0004)*
APOBEC 3G nonsynonymous allele frequencies (%)
H186R (rs8177832) A (H) G (R) 63.037.0 56 44 (P = 0.1147) 75 25 (P = 0.0249)* 49 51 (P = 0.0026)* 57 43 (P = 0.1344) 68 32 (P = 0.3013) 49 51 (P = 0.0030)* 52 48 (P = 0.0101)*
R256H (rs17000736) G (R) A (H) 98.8 1.2 98 2 (P = 0.7118) 98 2 (P = 0.6631) 99 1 (P = 0.6550) 97 3 (P = 0.1316) 98 2 (P = 1.0) 99 1 (P = 0.6660) 99 1 (P = 1.0)
Q275E (rs17496046) C (Q) G (E) 82.117.9 90 10 (P = 0.0026)* 91 9 (P = 0.0064)* 86 14 (P = 0.0725) 87 13 (P = 0.0482)* 83 17 (P = 0.3526) 91 9 (P = 0.0027)* 87 13 (P = 0.0473)*
G363R (rs148267053) G (G) A (R) 94.8 5.2 98 2 (P = 0.1066) 99 1(P = 0.0532) 100 0 (P = 0.0005)* 98 2(P = 0.0429)* 99 1(P = 0.0142)* 98 2 (P = 0.0902) 98 2 (P = 0.1209)
APOBEC3G synonymous allele frequencies (%)
S60S (rs112603901) C (S) T (S) 94.5 5.5 99 1 (P = 0.0027)* 98 2(P = 0.1191) 100 0 (P = 0.0002)* 100 0 (P = 0.0001)* 99 1 (P = 0.0026)* 100 0 (P = 0.0006)* 100 0 (P = 0.0001)*
A109A (rs375760983) C (A) T (A) 99.7 0.3 ND ND ND ND ND ND ND
F119F (rs5757465) T (F) C (F) 99.7 0.3 93 7 (P = 0.0001)* 89 11 (P = 0.0001)* 100 0(P = 1.0) 98 2 (P = 0.1639) 98 2 (P = 0.1507) 99 1 (P = 1.0) 99 1 (P = 0.5654)
L371 L (rs11545130) C (L) T (L) 97.9 2.1 98 2 (P = 0.7523) 98 2 (P = 1.0) 97 3 (P = 0.7698) 98 2 (P = 1.0) 95 5 (P = 0.1239) 98 2 (P = 1.0) 95 5 (P = 0.1299)
APOBEC 3H nonsynonymous allele frequencies (%)
N15Δ (rs140936762) CAA(N) Δ 40.2 59.8 71 29 (P < 0.0001)* 70 30 (P < 0.0001)* 61 39 (P = 0.0004)* 78 22 (P < 0.0001)* 62 38 (P = 0.0002)* 75 25 (P < 0.0001)* 68 32 (P < 0.0001)*
R18L (rs139293) G (R) T (L) 89.8 10.2 93 7 (P = 0.3230) 87 13 (P = 0.3885) 93 7 (P = 0.3212) 94 6 (P = 0.0972) 94 6 (P = 0.0873) 93 7 (P = 0.3053) 96 4 (P = 0.0076)*
G105R (rs139297) G (G) C (R) 2.2 97.8 15 85 (P < 0.0001)* 25 75 (P < 0.0001)* 10 90 (P = 0.0007)* 13 87 (P < 0.0001)* 9 91 (P = 0.0012)* 11 89 (P < 0.0002)* 9 91 (P < 0.0016)*
K121E (rs139298) A (K) G (E) 3.0 97.0 15 85 (P < 0.0001)* 25 75 (P < 0.0001)* 10 90 (P = 0.0025)* 13 87 (P < 0.0001)* 9 91 (P = 0.0070)* 11 89 (P = 0.0008)* 9 91 (P = 0.0086)*
K140E (rs139300) A (K) G (E) 0100 0100 (P = 1.0) 0100 (P = 1.0) 0100 (P = 1.0) 0100 (P = 1.0) 0100 (P = 1.0) 0100 (P = 1.0) 0100 (P = 1.0)
E178D (rs139302) G (E) C (D) 6.4 93.6 17 83 (P = 0.0004)* 29 71 (P < 0.0001)* 11 89 (P = 0.0900) 16 84 (P = 0.0007)* 16 84 (P = 0.0018)* 13 87 (P = 0.0248)* 11 89 (P = 0.0991)
APOBEC3H synonymous allele frequencies (%)
T43 T (rs139294) G (T) C (T) 7.1 92.9 22 78 (P < 0.0001)* 30 70 (P < 0.0001)* 16 84 (P = 0.0026)* 16 84 (P = 0.0024)* 13 87 (P = 0.0545) 17 83 (P = 0.0016)* 13 87 (P = 0.0439)*
  1. Note:
  2. NI = Not Identified previously
  3. ND = Not Determined in 1000 genomes database
  4. *= Significant (P value ≤0.05); Fisher’ s Exact Test used