TABLE 3.

Candidate rare Copy Number Variations likely associated with cancers.

Chromosome	Start	End	CNV length	CNV type	Genes	Affected Pathways		Network of Cancer genes annotation	DGV Frequency	AnnotSV ranking	Literature review
						Wikipathways	KEGG
3	48612641	48612972	-331	DEL	COL7A1	−	Protein digestion and absorption	Chronic myeloid leukemia	0.00017	4	COL7A1 gene is mutated and a candidate tumor suppressor gene in breast cancer. Hypermethylation of COL7A1 in breast cancer resulted in loss of ColVII expression in tumors correlating with a poor prognosis (Wood et al., 2007; Chan et al., 2008)
6	32147655	32147903	248	DUP	RNF5	−	Protein processing in endoplasmic reticulum	−	−	4	RNF5 is involved in the control of breast cancer progression and in survival of breast cancer patients (Bromberg et al., 2007). Ubiquitin ligase RNF5 serves an important role in the development of human glioma. RNF5 was significantly associated with diagnosis and prognosis of Hepatocellular carcinoma (Zhu et al., 2016; Gao et al., 2019)
12	88512261	88554006	41745	DUP	CEP290, TMTC3	Pathways in clear cell renal cell carcinoma	−	(TMTC3) A candidate cancer gene mutated in Pancreatic cancer	−	4	−
19	45261982	45262872	-890	DEL	BCL3	Apoptosis-related network due to altered Notch3 in ovarian cancer	C-type lectin receptor signaling pathway TNF signaling pathway	Hepatobiliary (Cholangiocarcinoma)	−	4	BCL3 participates in progression of diverse solid tumors (Maldonado and Melendez-Zajgla, 2011)

AnnotSV ranking: 4 Likely Pathogenic.