Spectrum of germline pathogenic variants using a targeted next generation sequencing panel and genotype-phenotype correlations in patients with suspected hereditary breast cancer at an academic medical centre in Pakistan

Akbar, Fizza; Siddiqui, Zahraa; Waheed, Muhammad Talha; Ehsan, Lubaina; Ali, Syed Ibaad; Wiquar, Hajra; Valimohammed, Azmina Tajuddin; Khan, Shaista; Vohra, Lubna; Zeeshan, Sana; Rashid, Yasmin; Moosajee, Munira; Jabbar, Adnan Abdul; Zahir, Muhammad Nauman; Zahid, Naila; Soomro, Rufina; Ullah, Najeeb Niamat; Ahmad, Imran; Haider, Ghulam; Ansari, Uzair; Rizvi, Arjumand; Mehboobali, Arif; Sattar, Abida; Kirmani, Salman

doi:10.1186/s13053-022-00232-2

Hereditary Cancer in Clinical Practice

Table 7 Pathogenic and likely pathogenic variants identified in genes other than BRCA1 and BRCA2

From: Spectrum of germline pathogenic variants using a targeted next generation sequencing panel and genotype-phenotype correlations in patients with suspected hereditary breast cancer at an academic medical centre in Pakistan

Serial No.	Patient ID	Age at diagnosis	Type	Gene	Variant Details	Exon	Consequence
1	44	29	U/L Breast Ca	ATM	c.8480 T > G (p.Phe2827Cys),	58	Missense
2	135	58, 63	B/L Breast Ca	BARD1	Deletion (Entire coding sequence)	Exon 1–11	LGR
3	169	40	U/L Breast Ca	BARD1	Deletion (Entire coding sequence)	Exon 1–11	LGR
4	20	41	U/L Breast Ca	CHEK2	c.58C > T (p.Gln20*)	2	Non-sense
5	96	35	U/L Breast Ca	CHEK2	Deletion (Exon 5)	Deletion of Ex. 5	LGR
6	165	60	B/L Breast Ca	CHEK2	c.409C > T (p.Arg137*)	3	Non-sense
7	225	40	U/L Breast Ca	CHEK2	c.58C > T (p.Gln20*)	2	Non-sense
8	21	44	U/L Breast Ca	CHEK2	c.283C > T (p.Arg95*)	2	Non-sense
8	21	44	U/L Breast Ca	RAD51C	c.701C > G (p.Ser234*)	4	Non-sense
9	243	56	U/L Breast Ca	FANCM	c.4153G > T (p.Glu1385*),	14	Non-sense
10	279	43	U/L Breast Ca	FANCM	c.2199_2202del (p.Ser734Asnfs*25),	13	Frameshift
11	11	43	U/L Breast Ca	MLH1	Deletion (Exon 16–19)	Deletion of Ex. 16–19	LGR
12	241	60	U/L Breast Ca	MLH1	c.1897-2A > G (Splice acceptor)	Intron 16	Splice acceptor
13	269	39	U/L Breast Ca	MLH1	c.306G > T (p.Glu102Asp)	3	Missense
14	102	30	U/L Breast Ca	MSH6	c.1222_1226del (p.Pro408Aspfs*8),	4	Frameshift
15	202	51	U/L Breast Ca	MUTYH	c.312C > A (p.Tyr104*)	3	Non-sense
16	248	48	U/L Breast Ca	MUTYH	c.312C > A (p.Tyr104*)	3	Non-sense
17	80	66	U/L Breast Ca	NF1	c.5205 + 5G > A	Intron 36	Splice donor
18	227	38	U/L Breast Ca	PALB2	c.2488del (p.Glu830Serfs*21),	5	Frameshift
19	258	42	U/L Breast Ca	PALB2	c.2353_2354del (p.Pro785Thrfs*16)	5	Frameshift
20	57	64	B/L Breast Ca	PALB2	c.2488del (p.Glu830Serfs*21)	5	Frameshift
21	18	34,37	B/L Breast Ca	RAD51D	c.898C > T, p.Arg300*,	9	Non-sense
22	144	55	U/L Breast Ca	RAD51D	c.620C > T (p.Ser207Leu)	7	Missense
22	144	55	U/L Breast Ca	FANCM	c.4318-1G > A (Splice acceptor)	Intron 15	Splice acceptor
23	184	40	U/L Breast Ca	TP53	c.537 T > G (p.His179Gln)	5	Missense
24	240	29	U/L Breast Ca	TP53	c.437G > A (p.Trp146*)	5	Non-sense

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