Table 5 Classification of detected variants by gene and cancer impact.
From: Evaluation of cfDNA as an early detection assay for dense tissue breast cancer
Genes | SNP ID | AF | Genomic structural | Functional annotation | Cancer related | BC related |
|---|---|---|---|---|---|---|
Pos-pos | ||||||
CNTN3 |  rs139142211 | 0.0004 | Coding | EX | – | – |
TMEM44 | rs146561237 | NA | Coding | EX | – | – |
ANK2 |  rs776254819 | NA | Coding | EX | – | – |
SERAC1 | rs757825963 | NA | Coding | EX | Blood | – |
DAGLB |  rs766835420 | NA | Coding | EX | Blood, Colorectal | – |
TNC |  rs376093344 | NA | Coding | EX | – | – |
MACF1 | NA | NA | Noncoding | INT | Liver, Blood, Pancreatic | – |
BATF3 | NA | NA | Noncoding | Upstream | – | – |
NVL | NA | NA | Noncoding | INT | Blood | – |
FBXW4 |  rs147494591 | 0.0078 | Noncoding | INT | Blood | – |
FANK1 | NA | NA | Noncoding | INT | Colorectal | – |
KCTD4 | NA | NA | Noncoding | 5’UTR | Colorectal | – |
SHF | NA | NA | Noncoding | Upstream | – | – |
CAVIN1; ATP6V0A1 | rs190711126 | 0.0004 | Noncoding | Intergenic | Blood, Colorectal, Pancreatic | – |
HIF3A | NA | NA | Noncoding | 5’UTR | – | – |
LOC101927050; LOC654342 |  rs11883680 | NA | Noncoding | Intergenic | – | – |
ZBTB20-AS1 | rs114892760 | 0.0032 | Noncoding | ncRNA_intronic | Liver, Blood, Pancreatic, Skin | – |
KMT2C |  rs2884935 | NA | Noncoding | INT | Liver, Blood, Pancreatic, Colorectal, Gastric | Breast |
Pos-neg | ||||||
SNIP1 | rs202020647 | 0.0002 | Coding | EX | Colorectal | – |
ATP2A1 | rs769732457 | NA | Coding | EX |  | – |
TBC1D10B |  rs145571848 | NA | Coding | EX | Blood, Colorectal | – |
EVPL | rs201833287 | 0.0002 | Coding | EX | – | – |
PANK1 | NA | NA | Noncoding | Upstream | Liver, Blood | – |
PRKCA | rs139323901 | 0.003 | Noncoding | INT | Blood, Colorectal, Pancreatic, Gastric | – |
RUNX2; SUPT3H | NA | NA | Noncoding | INT | Blood | – |
