TABLE 4.
Rare germline non-coding variants detected in HB patients which were prioritized (CADD score above 15 and association with cancer).
| ID | Gene | Genomic Coordinates* | Ref/Alt | Sequence Ontology | Variants | CADD Score | Inheritance | Co-Occurrence with Coding Variant |
|---|---|---|---|---|---|---|---|---|
| P02 | KLF12 | 13:74518363 | T/A | intron_variant | c.34–156A > T | 15.12 | N/A | |
| P02 | PRKCH | 14:61788795 | C/T | 5_prime_UTR_variant | c.-25C > T | 16.91 | not maternal | |
| P02 | BLMH | 17:28575944 | G/A | 3_prime_UTR_variant | c.*91C > T | 15.7 | N/A | |
| P02 | CARM1 | 19:11030266 | C/T | splice_region_variant | c.1021–5C > T | 15.69 | not maternal | |
| P10 | IKZF3 | 17:37949260 | C/T | intron_variant | c.164-74G > A | 15.38 | maternal | |
| P10 | PTPN1 | 20:49126913 | G/A | 5_prime_UTR_variant | c.-152G > A | 17.68 | N/A | |
| P10 | SEPSECS | 4:25161856 | G/A | intron_variant | c.114 + 22C > T | 16.15 | not maternal | |
| P15 | HES7 | 17:8026335 | G/A | intron_variant | c.138 + 14C > T | 15.59 | not maternal | |
| P15 | CNGB3 | 8:87755859 | C/T | 5_prime_UTR_variant | c.-4G > A | 15.68 | not maternal | |
| P18 | DLGAP1 | 18:3874312 | T/C | intron_variant | c.957 + 4800A > G | 16.45 | N/A | |
| P19 | FAM65C | 20:49206219 | T/C | splice_region_variant | c.2661+4A > G | 17.98 | not maternal | |
| P19 | BRAF# | 7:140453973 | T/A | intron_variant | c.1741 + 14A > T | 17.02 | not maternal | |
| P12 | TCF7 | 5:133451301 | C/T | 5_prime_UTR_variant | c.316 + 223C > T | 15.81 | de novo | yes [TCF7 VUS (c.1060C > G)] |
| P25 | UCP3 | 11:73715453 | G/T | intron_variant | c.643 + 76C > A | 19.81 | N/A | |
| P25 | ITGA7 | 12:56094605 | C/T | intron_variant | c.670 + 78G > A | 16.72 | N/A | |
| P25 | PPP1R12A | 12:80172901 | G/C | intron_variant | c.2956–521C > G | 18.05 | N/A | |
| P25 | NIN | 14:51297660 | G/C | intron_variant | c.-76 + 64C > G | 19.02 | N/A | |
| P25 | CREBBP# | 16:3811652 | G/A | intron_variant | c.3251–2679C > T | 16.15 | N/A | |
| P25 | CDK12 | 17:37618316 | G/A | 5_prime_UTR_variant | c.-9G > A | 18.03 | N/A | |
| P26 | PLK3 | 1:45269400 | C/T | intron_variant | c.1164 + 37C > T | 15.47 | not maternal | |
| P26 | SERPINI2 | 3:167184804 | A/T | intron_variant | c.508 + 39T > A | 17.66 | not maternal | |
| P26 | GFRA2 | 8:21645850 | G/C | 5_prime_UTR_variant | c.-179C > G | 18.32 | not maternal | |
| P26 | ZNF462 | 9:109692049 | A/G | intron_variant | c.5847+9A > G | 18.73 | not maternal |
#known/candidate cancer predisposition genes; *given according to GRCh37; N/A: not available.