Table 2.

Gold variants.

Chr	Position	Ref *	Alt *	Depths	Gene	LA +	Type	AA Chg	Pat	pLI	AF Lat §	ProtSize
11	108175579	G	A	21,19	ATM		Splice	E1892_E37	H4	0	1 × 10−4	3056
15	91341429	A	AG	15,25	BLM		Frameshift	T1074fs	D8	0	-	1417
17	41258472	C	A	54,35	BRCA1		Splice	R71_E4	G8	0	3 × 10−5	1863
13	32914033	CA	C	18,20	BRCA2		Frameshift	S1848fs	E0	0	3 × 10−5	3418
13	32914122	AC	A	52,30	BRCA2		Frameshift	N1877fs	J2	0	3 × 10−5	3418
13	32930653	C	CA	15,17	BRCA2		Frameshift	S2509fs	B2	0	-	3418
13	32937507	A	G	44,30	BRCA2		Missense	D2723G	G2	0	A:C 0	3418
13	32954260	CG	C	23,17	BRCA2		Frameshift	V3079fs	K5	0	2 × 10−4	3418
22	29091718	TA	T	29,23	CHEK2		Frameshift	L413fs	J6	0	-	543
22	29115401	A	ATGAT	28,16	CHEK2		Frameshift	M222fs	F5	0	1 × 10−4	543
22	19222211	C	T	33,36	CLTCL1	No	Missense	E330K	G5	0	9 × 10−4	1640
2	189868190	T	A	35,26	COL3A1	No	Splice	P869P	J6	1	9 × 10−5	1466
7	101926377	C	T	57,41	CUX1	No	Nonsense	Q678 *	G2	1	3 × 10−3	678
16	50818362	T	A	30,39	CYLD	No	Splice	I650_E13	C1	1	3 × 10−5	956
18	50734187	G	A	28,23	DCC	No	Splice	V621_E11	H2	0.99	2 × 10−4	1447
X	41206109	T	C	46,39	DDX3X	No	Splice	G539_E15	K3	1	4 × 10−5	662
X	41206562	T	C	44,41	DDX3X	No	Splice	S590_E16	F3	1	2 × 10−3	662
19	45917294	T	C	21,22	ERCC1		Splice	V235_E7	H0	0	6 × 10−5	297
10	50680422	C	T	16,25	ERCC6	No	Splice	R975_E16	G8	0	C:A 3 × 10−5	1493
11	44228353	G	A	33,34	EXT2	No	Nonsense	W535 *	A2	0	1 × 10−4	718
6	35425330	C	T	25,34	FANCE	No	Splice	D286_E3	A0	0	3 × 10−4	536
4	187530955	C	G	34,21	FAT1	No	Splice	T3356T	B0	0	0	4588
17	17117000	CG	C	45,40	FLCN	No	Frameshift	R570fs	C0	0.79	C:T 3 × 10−5	579
1	152285000	G	A	46,43	FLG	No	Nonsense	R788 *	K8	0	6 × 10−4	4061
1	152285861	G	A	45,34	FLG	No	Nonsense	R501 *	K1	0	4 × 10−3	4061
17	42148542	TC	T	11,14	G6PC3	No	Frameshift	I70fs	H0	0	8 × 10−4	346
14	62203827	G	A	20,20	HIF1A	No	Splice	D417_E9	A2	0	2 × 10−4	826
2	48033791	GT(26)	G	15,12	MSH6		Splice	R1334_E9	A0	0	1 × 10−4 &	1360
1	45797228	C	T	25,23	MUTYH		Splice	G396_E13	E7	0	3 × 10−3	546
6	44233331	G	GC	21,12	NFKBIE	No	Frameshift	A57fs	I9	0.77	3 × 10−4	500
5	176722446	TC(6)	T	27,25	NSD1	No	Frameshift	S2424fs	G7	1	-	2696
16	23641062	CAG	C	25,39	PALB2		Frameshift	S804fs	D6	0	1 × 10−4	1186
16	23641139	G	C	24,36	PALB2		Nonsense	S779 *	K6	0	9 × 10−5	1186
3	52620706	TG	T	15,12	PBRM1	No	Splice	E1017_E21	C9	1	0 &	1689
2	190728500	C	T	26,29	PMS1	No	Nonsense	R630 *	C9	0	1 × 10−4	932
3	121168273	T	C	19,22	POLQ		Splice	I2385V	B2	0	-	2590
3	121207489	A	T	20,15	POLQ		Nonsense	L1430 *	E6	0	9 × 10−5	2590
5	23527845	CA	C	31,42	PRDM9	No	Frameshift	T883fs	B6	0	6 × 10−5	894
1	45294985	C	T	14,13	PTCH2	No	Splice	L406_E10	B1	0	3 × 10−5	1203
17	56774167	C	CT	47,59	RAD51C		Frameshift	A173fs	A5	0	-	376
1	145507646	G	A	15,27	RBM8A	No	UTR_5	E1_UTR_5	G1	0.57	1 × 10−2	174
1	145507646	G	A	18,24	RBM8A	No	UTR_5	E1_UTR_5	G5	0.57	1 × 10−2	174
2	3623181	G	A	51,58	RPS7	No	Splice		E4	0.95	-	194
1	16262459	G	GC(27)	27,17	SPEN	No	Frameshift	A3242fs	I0	1	9 × 10−4 &	3664
17	7578406	C	T	22,29	TP53		Missense	R175H	I9	0.53	0	393
16	2124201	C	T	44,31	TSC2	No	Splice	R786C	B0	1	0	1807
17	5074956	T	A	83,62	USP6	No	Nonsense	Y1343 *	H3	0	9 × 10−5	1406
8	31014882	A	G	13,13	WRN		Splice	K1274_E33	J8	0	1 × 10−4	1432
16	72991713	C	CC(9)	20,14	ZFHX3	No	Frameshift	A778fs	H6	1	0	3703
X	70466308	GTGGT	G	28,11	ZMYM3	No	Frameshift	P821fs	L2	1	-	1370

* Numbers in parenthesis represent the total length. ⁺ Represent whether the gene has been reported in Latin-American BC patients in the Urbina-Lara et al. analysis [11]. ^§ Allele frequency in Latino population from GnomAD website (https://gnomad.broadinstitute.org/, accessed on 1 December 2021). Variants in GnomAD slightly different to those found are explicitly indicated or marked with ^&. A total of 50 variants is shown, 49 unique (RBM8A is present in two patients). Genomic positions correspond to hg19. Ref and Alt refer to reference and alternate alleles respectively. Depths refers to Ref and Alt alleles respectively. AA Chg refers to aminoacid change. Pat refers to patient. pLI refers to the probability of LoF intolerance. ProtSize refers to canonical transcript protein size in aminoacids. Bold genes mark those found more than once. AF Lat = Allele Frequency in Latin Americans.