Table 2 Rare Potentially Oncogenic Variants (POVs) identified in 217 African ancestral prostate cancer (PCa) patients from the SAPCS (n = 186) and PPCG (n = 31) study cohorts and impacting 16 known and/or Potentially Pathogenic Variants (PPVs) recognised in DNA Damage Repair (DDR) germline testing genes

From: Pathogenic variants reveal candidate genes for prostate cancer germline testing for men of African ancestry

Gene	Chr position: nt change	rsID^a	AA Change	VAF^b	SAPCS (n)	PPCG (n)	AFR Fraction^c	MAF SAC (n = 49)^d	MAF EAC (n = 40)^d
BRCA2	chr13:32341158:G/A	rs80358906	R2268K	0.59	0	1	66%	0	0
	chr13:32357808:A/T	rs80358995	F2562I	ND	0	1	>99%	0	0
	chr13:32370460:A/G	unknown	D2797G	0.52	0	1	93%	0	0
PMS2	chr7:5982890:G/A	rs370196722	T703M	ND	0	1	57%	0	0
	chr7:6003981:C/T	rs730881919	E81K	0.576923	1	0	>99%	0	0
FANCA	chr16:89769976:C/T	rs771698195	V879M	ND	0	1	57%	0	0
	chr16:89783063:G/A	rs200291237	R504G	0.560976	1	0	>99%	0	0
BARD1	chr2:214767537:C/T	rs864622240	G486R	0.404255	1	0	>99%	0	0
	chr2:214809476:C/G	rs1224914625	G32R	0.512195	1	0	>99%	0	0
ATM	chr11:108253834:AAAG/A	rs876659575	E642del	All(2) > 0.44	2	0	Both>99%	0	0
MSH6	chr2:47806344:G/A	rs367912290	R961C	0.431818	1	0	>99%	0	0
PALB2	chr16:23626343:C/T	rs766315705	G586S	0.571429	1	0	98%	0	0
POLE	chr12:132642888:C/T	rs143247306	E1554K	0.516129	1	0	>99%	0	0
	chr12:132648934:G/A	rs5744904	R1355C	0.454545	1	0	>99%	0.0102041	0
	chr12:132649341:G/A	rs779464847	R1297C	All(2) > 0.57	2	0	Both>99%	0.0102041	0
	chr12:132664038:G/C	rs2042735587	S864C	0.38	1	0	>99%	0	0
	chr12:132672668:A/G	rs115558715	S549P	0.447368	1	0	>99%	0	0
	chr12:132680212:G/A	rs5744739	P99L	All(3) > 0.52	3	0	>99%(2),97%	0	0
LRP1B	chr2:140442513:C/T	rs144998818	A3469T	All(3) = 0.54	3	0	>99%(2),98%	0.0102041	0.0125
	chr2:140475215:T/C	rs1687922196	Y3183C	0.531915	1	0	>99%	0	0
	chr2:140598725:C/T	unknown	G2367E	0.560976	1	0	>99%	0	0
	chr2:140841014:G/A	rs199519370	T1673M	0.459459	1	0	>99%	0	0
	chr2:140886324:C/T	rs752553135	A1260T	0.584906	1	0	>99%	0	0
ROS1	chr6:117319878:A/G	rs145889490	V1977A	0.536585	1	0	>99%	0	0
	chr6:117337265:G/T	rs369993254	L1719I	ND	0	1	78%	0	0
	chr6:117342504:G/T	rs112739824	P1522Q	0.666667	1	0	>99%	0.0102041	0
	chr6:117365621:C/A	rs370129182	G978V	All(3) > 0.51	3	0	All>99%	0	0
RET	chr10:43120084:G/A	rs145170911	V871I	0.617647	1	0	>99%	0	0
	chr10:43121991:C/G	rs774215008	H926D	0.454545	1	0	98%	0	0
	chr10:43123801:G/A	rs758800351	E978K	ND	0	1	67%	0	0
JAK2	chr9:5078384:A/C	rs151160183	N691H	0.45	0	1	85%	0	0
	chr9:5090448:C/T	rs764302764	R922W	0.509091	1	0	>99%	0.0204082	0
MSH3	chr5:80873226:G/A	rs1328941442	Splice variant	All(3) > 0.44	3	0	All>99%	0	0
EGFR	chr7:55142300:A/G	unknown	S35G	0.55	1	0	>99%	0	0
TRRAP	chr7:98976168:C/G	rs143477790	A2335G	All(3) > 0.47	3	0	>99%	0	0
ERBB3	chr12:56094550:C/G	rs757518347	T618S	All(3) > 0.38	3	0	All>99%	0	0

AA amino acid, AFR African, chr chromosome, EAC East African Control, MAF minor allele frequency, nt nucleotide, PPCG Pan Prostate Cancer Group, SAC Southern African Control, SAPCS Southern African Prostate Cancer Study, VAF variant allele frequency.
^aUnknown rs-numbers are absent from variant databases.
^bExclusion based on CHIP-likelihood (VAF < 0.3).
^cAfrican ancestral fraction presented as a percentage (southern, western and/or San) and k = 4 ADMIXTURE plot (Fig. 1).
^dMAF for population-relevant controls. Known PCa germline testing panel genes include BRCA2, PMS2, FANCA, BARD1, ATM, MSH6 and PALB2.

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