Table 2.
Candidate variants (HGVS) in cancer-susceptibility genes observed in the cohort after filtering.
| Gene name | HGVS nomenclature | Exonic Function | CADD1.4 Phred | gnomAD all freq | ClinVar | InterVar | rs |
|---|---|---|---|---|---|---|---|
| Diagnostic variants related to the phenotype | |||||||
| BRCA1 | NM_007294.3:c.2933dupA p.(Tyr978Ter) | stopgain | . | . | P | . | rs878853292 |
| BRCA1 | NM_007294.3:c.843_846delCTCA p.(Ser282Tyr) | frameshift deletion | . | . | P | . | rs80357919 |
| BMPR1A | NM_004329.2:c.1439 G > T p.(Arg480Leu) | missense | 33 | . | VOUS | VOUS | rs535109719 |
| FANCA | NM_000135.4:c.295 C > T p.(Gln99Ter) | stopgain | 36 | . | P | rs1057516430 | |
| FANCC | NM_000136.2:c.37 C > T p.(Gln13Ter) | stopgain | 36 | . | P/LP | P | rs121917784 |
| NBN | NM_002485.4:c.657_661delACAAA p.(Lys219AsnfsTer16) | Frameshift deletion | . | 0.00030 | P | . | rs587776650 |
| Pathogenic and likely pathogenic variants unrelated to the phenotype (incidental) - reported to patients | |||||||
| BRCA2 | NM_000059.3:c.8331 + 1 G > A | - | 34 | P | . | rs81002837 | |
| PALB2 | NM_024675.3:c.93dupA p.(Leu32ThrfsTer11) | frameshift insertion | . | . | P/LP | . | rs864622498 |
| RAD50 | NM_005732.3:c.3050 G > A p.(Trp1017Ter) | stopgain | 45 | . | P | P | . |
| Pathogenic and likely pathogenic variants NOT reported to patients | |||||||
| ATR | NM_001184.3:c.7273 C > T p.(Arg2425Ter) | stopgain | 43 | . | . | P | rs1310011888 |
| BLM | NM_000057.3:c.1642C > T p.(Gln548Ter) | stopgain | 35 | 0.00040 | P/LP | P | rs200389141 |
| FANCB | NM_152633.3:c.2254 G > T p.(Glu752Ter) | stopgain | 39 | 0.00010 | . | P | |
| MUTYH | NM_001128425.1:c.1437_1439delGGA p.(Glu480del) | Non-frameshift deletion | . | 0.0000323 | p | . | rs587778541 |
| XPC | NM_004628.4:c.1677C > A p.(Tyr559Ter) | stopgain | 36 | . | P | P | rs767569346 |
| Secondary findings NOT reported to patients -with high likelihood for pathogenicity | |||||||
| BLM | NM_000057.4:c.3062 A > G p.(Asn1021Ser) | missense | 23.1 | . | VOUS | VOUS | rs369629509 |
| BRCA1 | NM_007294.3:c.2666 C > T p.(Ser889Phe) | missense | 18.58 | . | Conflicting interpretations | VOUS | rs769712441 |
| BRCA2 | NM_000059.3:c.8735 C > T p.(Ala2912Val) | missense | 23.7 | . | . | VOUS | . |
| BRCA2 | NM_000059.3:c.8320 C > G p.(Leu2774Val) | missense | 26.5 | . | . | VOUS | . |
| CHEK2 | NM_007194.4:c.482 A > G p.(Glu161Gly) | missense | 28.1 | . | VOUS | VOUS | rs730881683 |
| DICER1 | NM_030621.4:c.3591 C > G p.(Cys1197Trp) | missense | 24.6 | . | . | VOUS | . |
| ERCC4 | NM_005236.2:c.934 T > G p.(Ser312Ala) | missense | 25.9 | 0.0000646 | . | . | rs200596978 |
| MLH1 | NM_000249.3:c.41 C > T p.(Thr14Ile) | missense | 24.5 | . | VOUS | VOUS | rs774363593 |
| RET | NM_020975.6:c.2330 A > G p.(Asn777Ser) | missense | 20.6 | . | VOUS | VOUS | rs377767415 |
| SDHB | NM_003000.2:c.230 T > A p.(Ile77Asn) | missense | 29.6 | . | . | VOUS | . |
| TP53 | NM_000546.5:c.665 C > T p.(Pro222Leu) | missense | 19.42 | 0.0000646 | VOUS | VOUS | rs146340390 |
HGVS = Human Genome Variation Society; Freq = frequency; P = Pathogenic; LP = Likely Pathogenic, VOUS = variant of unknown significance.