Table 2.
P/LP GVs
| Patient ID | Paired material | Gene name (RefSeq) | HGVS.c | HGVS.p | dbSNP | Germ line VAF | Tumoral VAF | ClinVar | CADD | MutationTaster | GnomAD WG AF POPMAX |
ACMG-AMP criteria | Clinical variant classification |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AQ5388 | Saliva | DDX41 (NM_016222.4) | c.804delG | p.Glu268fs | rs780979459 | 0.53 | 0.45 | NA | NA | NA | PVS1 + PM2 | LP | |
| AQ5389 | PRBM | DDX41 (NM_016222.4) | c.1015C>T | p.Arg339Cys | rs759862062 | 0.56 | 0.49 | NA | 32 | Disease causing (1) | NA | PM1 + PM5 + PP2 + PP3 | LP |
| AQ5357 | BMSC | ATM (NM_000051.4) | c.1110C>G | p.Tyr370∗ | rs376170600 | 0.52 | 0.51 | P | 25 | Disease causing automatic (1) | NA | PVS1 + PM2 + PP5 | P |
| AQ5355 | BMSC | ATM (NM_000051.4) | c.2672C>G | p.Ser891∗ | rs876660780 | 0.58 | 0.5 | P | 36 | Disease causing automatic (1) | NA | PVS1 + PM2 + PP5 | P |
| AQ5358 | BMSC | ATM (NM_000051.4) | c.4148C>A | p.Ser1383∗ | rs141087784 | 0.53 | 0.5 | P/LP | 37 | Disease causing automatic (1) | NA | PVS1 + PM2 + PP5 | P |
| AQ5329 | BMSC | CHEK2 (NM_007194.4) | c.593-1G>T | rs786203229 | 0.45 | 0.48 | P/LP | 34 | Disease causing (1) | NA | PVS1 + PP5 + PM2 | P | |
| AQ5380 | BMSC | FANCM (NM_020937.4) | c.5791C>T | p.Arg1931∗ | rs144567652 | 0.47 | 0.54 | C | 42 | Disease causing automatic (1) | 0.0007422 | PVS1 + PM2 | LP |
| AQ5336 | PRBM | FANCA (NM_000135.4) | c.2529C>G | p.Tyr843∗ | rs1247378731 | 0.49 | 0.45 | P | 33 | Disease causing automatic (1) | NA | PVS1 + PM2 + PP5 | P |
| AQ5325 | BMSC | SBDS (NM_016038.4) | c.258+2T>C | rs113993993 | 0.57 | 0.54 | P/LP | 33 | Disease causing automatic (1) | 0.003675 | PVS1 + PM2 + PP5 + PS3 | P | |
| AQ5361 | BMSC | DNAJC21 (NM_001012339.3) | c.544C>T | p.Arg182∗ | rs771063992 | 0.53 | 0.55 | P | 37 | Disease causing automatic (1) | 0.00001171 | PVS1 + PM2 + PP5 | P |
| AQ5347 | BMSC | CSF3R (NM_000760.4) | c.296_299delTCTC | p.Leu99fs | NA | 0.63 | 0.49 | NA | NA | NA | PVS1 + PM2 | LP |
CADD, combined annotation dependent depletion; HGVS, Human Genome Variation Society; ID, identifier; PM, pathogenicity moderate; PP, pathogenicity supporting; PVS, pathogenicity very strong.