Table 2.
Summary of the 53 variants studied by our targeted RNA panel.
| Gene | Variant | p. | Splice prediction SpIP v2.1 | Splice prediction SpliceAI v1.3 | Splice effect RNA panel |
Splice effect Other criteria |
r. | NMD exclusion | ACMG criteria | Variant classification |
|---|---|---|---|---|---|---|---|---|---|---|
| APC | c.7500G>A | p.(Gln2500=) | Alter by creating de novo splice site 05.56% [01.91%-15.11%] | AG: 0.00; AL: 0.01; DG: 0.00; DL: 0.00 | Normal | / | r.7500G>A; p.(Gln2500=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| ATM | c.2922-2A>G | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.50; AL: 0.98; DG: 0.00; DL: 0.01 | Acceptor site modification | Confirmed by RT-PCR | r.2922_2953del; p.(Asn975Cysfs∗3) |
/ | PM2, PVS1 | 4 |
| ATM | c.7896C>T | p.(Asn2632=) | NTR 07.62% [04.42%-12.08%] | AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.01 | Normal | Confirmed by RT-PCR | r.7896C>T; p.(Asn2632=) | Heterozygous variant in RNA | PM2, BP4, BP7_S | 2 |
| ATM | c.4909+3G>A | p.? | Alteration of the consensus splice site 85.91% [79.27%-91.06%] |
AG: 0.00; AL: 0.00; DG: 0.35; DL: 0.14 | Normal | Confirmed by RT-PCR | r.= | Heterozygous variant in RNA | PM2, PP3, BP7_S | 2 |
| ATM | c.2377-6T>A | p.? | Alteration of the consensus splice site 30.67% [23.41%-38.71%] |
AG: 0.04; AL: 0.03; DG: 0.00; DL: 0.00 | Normal | / | r.= | / | PM2, BP7_S | 2 |
| ATM | c.8671+2_8671+3insTA | p.? | NA | NA | Exon 59 skipping | Confirmed by RT-PCR Co-segregation with breast cancer (29) |
r.8585_8671del; p.(Val2862_Leu2890del) | / | PM2, PP1, PVS1 | 5 |
| ATM | c.7785T>C | p.(Asp2595=) | NTR 05.05% [02.45%-09.09%] |
AG: 0.00; AL: 0.00; DG: 0.01; DL: 0.00 | Normal | / | r.7785T>C; p.(Asp2595=) | / | PM2, BP7_S | 2 |
| ATM | c.2679A>G | p.(Gln893=) | Alteration of an exonic splicing regulatory element 35.81% [28.11%-44.1%] |
AG: 0.00; AL: 0.01; DG: 0.00; DL: 0.00 | Normal | / | r.2679A>G; p.(Gln893=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| ATM | c.2124+1G>T | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.00; DG: 0.02; DL: 1.00 | Exon 13 skipping | Confirmed by RT-PCR | r.1899_2124del; p.(Cys633∗) | / | PM2, PVS1 | 4 |
| ATM | c.2839-1G>T | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.29; AL: 0.89; DG: 0.00; DL: 0.00 | Cryptic acceptor site creation | Confirmed by RT-PCR Identified in AT patient |
r.2839_2856del; p.(Tyr947_Lys952del) | / | PM2, PVS1_M, PM3 | 4 |
| ATM | c.8010+30insN[?] | p.? | NA | NA | Partial exon 54 skipping | Confirmed by RT-PCR | p.? | / | PM2, PVS1_NA | 3 |
| ATM | c.3078-30_3078-27del | p.? | Alter BP 42.50% [32.25%-53.43%] | AG: 0.03; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.= | No heterozygous variant | PM2, BP7_NA | 3 |
| ATM | c.7375C>G | p.(Arg2459Gly) | Alter ESR 35.81% [28.11%-44.1%] | AG: 0.00; AL: 0.00; DG: 0.14; DL: 0.01 | Normal | / | r.7375C>G; p.(Arg2459Gly) | Heterozygous variant in RNA | PM2, BP7_NA | 3 |
| BAP1 | c.720G>A | p.(Lys240=) | NTR 05.46% [04.02%-07.38%] | AG: 0.00; AL: 0.11; DG: 0.00; DL: 0.01 | Normal | / | r.720G>A; p.(Lys240=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| BAP1 | c.-9C>A | p.? | Alter ESR 30.18% [25.47%-35.35%] | AG: 0.00; AL: 0.01; DG: 0.00; DL: 0.00 | Normal | / | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| BRCA1 | c.2518A>T | p.(Ser840Cys) | NTR 01.24% [00.71%-02.15%] | AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.2518A>T; p.(Ser840Cys) | Heterozygous variant in RNA | PM2, BP7_NA | 3 |
| BRCA2 | c.9648+1G>A | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.00; DG: 0.01; DL: 1.00 | Exon 26 skipping | Confirmed by RT-PCR and mini-gene | r.9502_9648del; p.(Asn3168_Leu3216del) | / | PM2, PVS1_M | 3 |
| BRCA2 | c.8332-28A>G | p.? | Alteration of the branch point 23.61% [16.94%-31.4%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | Confirmed by RT-PCR | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| BRCA2 | c.7670C>T | p.(Ala2557Val) | NTR 07.81 % [04.44%-12.56%] (SpIP v1: alter ESR 28.87% [24.29%-33.93%]) |
AG: 0.04; AL: 0.02; DG: 0.00; DL: 0.18 | Normal | / | r.7670C>T; p.(Ala2557Val) | / | PM2, BP7_NA | 3 |
| BRCA2 | c.7524C>T | p.(Gly2508=) | NTR 07.8% [04.53%-12.37%] (SpIP v1: alter ESR + alter by creating de novo splice site 28.87% [24.29%-33.93%]) |
AG: 0.06; AL: 0.00; DG: 0.06; DL: 0.00 | Normal | / | r.7524C>T; p.(Gly2508=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| BRCA2 | c.68-8_68-7delinsAA | p.? | NA | NA | Partial exon 3 skipping | Confirmed by RT-PCR | p.? | / | PM2, PVS1_NA | 3 |
| BRCA2 | c.6842-8_6842-7del | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.43; DG: 0.00; DL: 0.00 | Total exon 12 skipping | Confirmed by RT-PCR | r.6842_6937del; p.(Glu2282_Gly2313del) | / | PM2, PVS1_M | 3 |
| CDH1 | c.1901C>T | p.(Ala634Val) | + Creation of a new splice site + alteration of an exonic splicing regulatory element 98.41% [91.47%-99.96%] | AG: 0.00; AL: 0.00; DG: 0.91; DL: 0.53 | Cryptic donor site creation | Confirmed in bibliography (13) | r.1900_1936del; p.(Ala634Profs) | / | PM2, PVS1, PP5 | 5 |
| CDH1 | c.906C>T | p.(Tyr302=) | NTR 07.8% [04.53%-12.37%] |
AG: 0.00; AL: 0.00; DG: 0.01; DL: 0.00 | Normal | / | r.906C>T; p.(Tyr302=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| CHEK2 | c.846+4_846+7del | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.98 (8) | Exons 7_8 skipping + exon 7 skipping | Confirmed by RT-PCR Confirmed in bibliography (30,31) |
r.793_908del; p.(Asp265Alafs∗7) r.793_846del; p.(265_282del) |
/ | PM2, PVS1, PS3 | 5 |
| CHEK2 | c.538C>T | p.(Arg180Cys) | Alteration of an exonic splicing regulatory element 35.81% [28.11%-44.1%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | Confirmed by RT-PCR | r.538C>T; p.(Arg180Cys) | / | PM2, BP7_NA | 3 |
| FLCN | c.-113-1G>A | p? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.42; AL: 0.95; DG: 0.00; DL: 0.00 | Exon 3 skipping (5'UTR) | / | r.-113_-25del; p.? | / | PM2, PVS1_NA | 3 |
| MLH1 | c.791-489_791-20del | p.? | Alter BP + alter by creating cryptic 36.17% [26.46%-45.88%] | NA | Partial exon 10 skipping | RT-PCR : partial exon 10 skipping Mini-gene : total exon 10 skipping |
r.791_884del; p.(His264Leufs∗2) | No heterozygous variant | PM2, PVS1_S, PP4, PP1 | 4 |
| MLH1 | c.306+5G>T | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] | AG: 0.00; AL: 0.00; DG: 0.12; DL: 0.79 | Cryptic donor site creation | RT-PCR: partial effect Mini-gene: total effect |
r.302_306del; p.(Glu102Phefs∗18) | No heterozygous variant | PM2, PVS1, PM5 | 5 |
| MLH1 | c.882C>G | p.(Leu294=) | Alteration of the consensus splice site 85.91% [79.27%-91.06%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.05 | Partial exon 10 skipping | Partial effect confirmed by RT-PCR Partial effect confirmed by mini-gene in bibliography (12) |
p.? | / | PM2, PVS1_NA | 3 |
| MLH1 | c.117-16_117-15del | p.? | Alteration of the polypyrimidine tract (-20 to -18) 23.61% [16.94%-31.4%) | AG: 0.00; AL: 0.02; DG: 0.00; DL: 0.00 | Normal | / | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| MLH1 | c.1897-42C>T | p.? | Alteration of the branch point 43.04% [35.2%-51.14%] AG:0.03; AL:0.00;DG:0.00;DL:0.00 |
AG: 0.03; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| MSH2 | c.793G>A | p.(Val265Ile) | Alteration of the consensus splice site 35.81% [28.11%-44.1%] |
AG: 0.03; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | Confirmed by RT-PCR | r.793G>A; p.(Val265Ile) | Heterozygous variant in RNA | PM2, BP7_NA | 3 |
| MSH6 | c.3537C>G | p.(Ala1179=) | NTR 08.25% [04.79%-13.05%] | AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | Confirmed by RT-PCR | r.3537C>G; p.(Ala1179=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| MSH6 | c.3173-22C>G | p.? | Alter BP 13.87% [08.56%-20.81%] |
AG: 0.01; AL: 0.03; DG: 0.00; DL: 0.00 | Normal | / | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| MSH6 | c.153C>T | p.(Ser51=) | NTR 03.43% [01.39%-06.94%] | AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.153C>T; p.(Ser51=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| MUTYH | c.1103-27C>T | p.? | Alter BP 98.11% [94.59%-99.61%] | AG: 0.01; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| NF1 | c.731-8del | p.? | Alteration of the consensus splice site 23.61% [16.94%-31.4%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.= | No heterozygous variant | PM2, BP7_NA | 3 |
| NF1 | c.2252-16del | p.? | NTR 05.74% [02.81%-11.37%] | AG: 0.00; AL: 0.03; DG: 0.00; DL: 0.00 | Normal | / | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| NF2 | c.1122+6T>C | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96 %] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.01 | Normal | Confirmed by RT-PCR | r.= | No heterozygous variant | PM2, BP7_NA | 3 |
| NF2 | c.1000-7C>G | p.? | Alteration of the consensus splice site 30.67% [23.41%-38.71%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.= | No heterozygous variant | PM2, BP7_NA | 3 |
| PALB2 | c.2379C>T | p.(Gly793=) | NTR 03.48% [01.41%-07.04%] | AG: 0.01; AL: 0.00; DG: 0.66; DL: 0.00 | Normal | / | r.2379C>T; p.(Gly793=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| PMS2 | c.23+1G>T | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.00; DG: 0.37; DL: 0.99 | Intronic retention | RT-PCR failure (pseudogene) Tumor PMS2 loss |
r.?; p.? | No heterozygous variant | PM2, PVS1, PP4 | 5 |
| PMS2 | c.1004A>G | p.(Asn335Ser) | NTR 09.76% [06.06%-14.67%] |
AG: 0.00; AL: 0.00; DG: 0.01; DL: 0.00 | Normal | / | r.1004A>G; p.(Asn335Ser) | Heterozygous variant in RNA | PM2, BP7_NA | 3 |
| PMS2 | c.803+5G>A | p.? | Alteration of the consensus splice site 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.00; DG: 0.01; DL: 0.98 | Partial crytic acceptor site use (r.762_803del) | Confirmed by RT-PCR | r.?; p.? | No heterozygous variant | PM2, PVS1_NA | 3 |
| POLE | c.5678+6G>A | p.? | Alteration of the consensus splice site 30.67% [23.41%-38.71%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | Confirmed by RT-PCR | r.= | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| PTEN | c.209+6T>G | p.? | Alteration of the consensus splice site 98.54% [94.83%-99.82%] |
AG: 0.00; AL: 0.77; DG: 0.00; DL: 0.85 | Exon 3 skipping | Confirmed by RT-PCR and mini-gene | r.165_209del; p.(Arg55_Leu70delinsSer) | No heterozygous variant | PM2, PVS1 | 4 |
| RAD51C | c.1026+5_1026+7del | p.? | Alteration of the consensus splice site 98.54% [94.83%-99.82 %] |
AG: 0.00; AL: 0.00; DG: 0.09; DL: 0.88 | Exon 8 skipping | Confirmed by RT-PCR | r.966_1026del; p.(Arg322Serfs∗22) | No heterozygous variant | PM2, PVS1, PP5 | 5 |
| RAD51C | c.513C>T | p.(Asp171=) | NTR 04.35% [02.01 %-08.09%] | AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.513C>T; p.(Asp171=) | Heterozygous variant in RNA | PM2, BP7_S | 2 |
| SDHA | c.762_770+17del | p.(Ala255_Gly257del) | Alteration of the consensus splice site + alteration of an exonic splicing regulatory element 98.41% [91.47%-99.96%] |
NA | Multiple complex alterations | / | r.?; p.? | / | PM2, PVS1 | 4 |
| SDHB | c.541-27T>G | p.? | NTR 09.76% [06.06%-14.67%] |
AG: 0.00; AL: 0.00; DG: 0.00; DL: 0.00 | Normal | / | r.= | No heterozygous variant | PM2, PVS1_NA | 3 |
| SDHC | c.19A>G | p.(Arg7Gly) | + Alteration of the consensus splice site + alteration of an exonic splicing regulatory element 98.41% [91.47%-99.96%] |
AG: 0.00; AL: 0.00; DG: 0.01; DL: 0.66 | Partial intronic retention | r.?; p.? | / | PM2, PVS1_M | 3 | |
| TMEM127 | c.-112G>T | p.? | NTR 04.63% [02.81%-07.14%] |
AG: 0.01; AL: 0.17; DG: 0.00; DL: 0.00 | Normal | / | r.= | No heterozygous variant | PM2, PVS1_NA | 3 |