Table 1 Rare Potentially Pathogenic Variants (PPVs, n = 45) identified in 217 African ancestral prostate cancer (PCa) patients impacting 34 DNA damage repair (DDR) or PCa related genes and as such further classified as known or candidate germline testing (GT) 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)	MAF EAC (n = 40)
BRCA2 ^d	chr13:32319100:T/C	rs80359182	W31R	0.439024	1	0	>99%	0	0
	chr13:32337185:A/T	rs80358533	K944X	0.642857	1	0	>99%	0	0
	chr13:32340123:ACATT/A	rs80359535	I1924fs	0.627907	1	0	>99%	0	0
	chr13:32340123:CTG/C	rs80359478	V1681fs	0.4	0	1	73%	0	0
	chr13:32363421:T/G	rs80359070	L2740X	0.27907	1	0	>99%	0	0
	chr13:32371013:AAAGG/A	rs397507406	Q2850fs	ND	0	1	89%	0	0
ATM ^d	chr11:108345818:C/T	rs587779872	R2832C	ND	0	1	87%	0	0
ATM ^d	chr11:108365476:C/T	rs121434219	R3047X	All(2) > 0.4722	2	0	>99%	0	0
RAD54L ^d	chr1:46250063:C/T	rs530382665	R52W	ND	0	1	57%	0	0
RAD54L ^d	chr1:46260594:C/T	rs149141765	R64W	0.461538	1	0	>99%	0	0
RAD50 ^d	chr5:132595759:T/TA	rs397507178	E723fs^e	0.526316	1	0	>99%	0	0.0125
TP53 ^d	chr17:7673776:G/A	rs28934574	R123W	0.209302	1	0	>99%	0	0
CHEK2 ^d	chr22:28734439:G/A	rs587781269	R283X^e	0.478261	1	0	>99%	0	0
NBN ^d	chr8:89978304:CA/C	rs1586101561	C167fs	ND	0	1	98%	0	0
RECQL4	chr8:144513050:TG/T	rs1024114400	P851fs	ND	0	1	67%	0	0
	chr8:144513139:C/T	rs398124117	Splice variant	0.555556	1	0	>99%	0	0
	chr8:144513260:ACGCCCGGCC/A	rs766312203	RAGR804-807R	All(2) > 0.3541	2	0	>99%	0.0102041	0.0125
FANCD2	chr3:10047980:C/T	rs755992976	Q448X	0.530612	1	0	>99%	0	0
FANCD2	chr3:10085886:CAG/C	rs770686014	Q1100fs	0.49	0	1	88%	0	0
TRRAP	chr7:98910216:C/CA	rs1797006154	A505fs	0.137931	1	0	>99%	0	0.0125
TRRAP	chr7:98910234:CG/C	rs2116406452	P512fs	0.0909091	1	0	>99%	0	0
CHD1L	chr1:147287651:G/A	unknown	W746X	0.47	1	0	>99%	0	0
ASPM	chr1:197121974:G/A	rs140602858	R1271X	0.648148	1	0	>99%	0	0
LRP1B	chr2:140850147:G/A	rs1692413234	R1632X	0.517241	1	0	>99%	0	0
ERBB4	chr2:211383652:G/A	rs751834116	P1297L	ND	0	1	68%	0	0
MSH3	chr5:80741503:TAATT/T	rs2112866803	I537fs	0.558824	1	0	>99%	0	0
ROS1	chr6:117310147:A/T	rs2128548191	L2123H	0.529412	1	0	>99%	0	0
EGFR	chr7:55191740:C/T	rs371228501	R831C	0.56	1	0	>99%	0	0
PREX2	chr8:68022072:A/C	unknown	N125H	0.444444	1	0	>99%	0	0
MYC	chr8:127740711:C/T	rs2130105792	T373I	0.5	1	0	>99%	0	0
JAK2	chr9:5072609:C/A	rs149705816	H587N	0.465116	1	0	>99%	0	0
APTX	chr9:33001566:C/A	rs146487634	Splice variant	All(4) > 0.4	3	1	>99%(3),92%	0	0
FANCG	chr9:35077266:TGGCGGTA/T	rs587776640	YRQ213-215fs	All(2) > 0.42	2	0	Both>99%	0	0
RET	chr10:43119548:G/A	rs79658334	V804M^f	0.545455	1	0	>99%	0	0
CHD4	chr12:6601528:G/A	unknown	P180L	0.48	1	0	>99%	0	0
ERBB3	chr12:56097837:G/A	rs771520731	R838Q	0.434783	1	0	>99%	0	0
POLE	chr12:132649751:C/A	rs779261309	E1241X	0.613636	1	0	>99%	0	0
BUB1B	chr15:40217665:T/C	unknown	Q964X	0.45	1	0	>99%	0	0
INO80	chr15:40987186:C/T	rs199722402	R1246Q	0.48	0	1	90%	0	0
BLM	chr15:90749728:T/TG	unknown	W154Wfs	0.44	1	0	>99%	0	0
NF1	chr17:31260369:GT/G	rs1555618803	F1478X	0.6	1	0	>99%	0	0
JAK3	chr19:17836001:G/A	rs149316157^e	R613X	0.47	1	0	>99%	0	0
DONSON	chr21:33586090:A/G	rs1010722195	F165S	0.52	0	1	>99%	0	0
U2AF1	chr21:43094667:T/G	rs371246226	Q157P^e	0.37	0	1	93%	0	0
STAG2	chrX:124066174:G/T	rs1603095192	Splice variant^f	1	1	0	>99%	0	0

AA amino acid, AFR African, chr chromosome, EAC east African Controls, MAF minor allele frequency, ND not determined, nt nucleotide, PPCG Pan Prostate Cancer Group, SAC southern African Controls, SAPCS Southern African Prostate Cancer Study, VAF variant allele frequency.
^aUnknown rs-numbers are absent from variant databases.
^bPPV exclusion based on CHIP-likelihood (VAF < 0.3).
^cAfrican ancestral genetic fraction presented as a percentage (southern, western and/or San) and k = 4 ADMIXTURE plot (Fig. 1).
^dKnown candidate germline testing gene.
^ePresent in a single European PPCG patient of 959.
^fPresent in a single European MGRB healthy control of 3209.

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Table 1 Rare Potentially Pathogenic Variants (PPVs, n = 45) identified in 217 African ancestral prostate cancer (PCa) patients impacting 34 DNA damage repair (DDR) or PCa related genes and as such further classified as known or candidate germline testing (GT) genes

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