Table 1.
Deep intronic variants leading to pseudoexonification of breast cancer genes
| Family | Variant | Genomic position (GRCh38) | No. of noncancer gnomAD v.3.1.2 | Previous ClinVar interpretationsa | ClinVar variant ID | Pseudoexon coordinates based on long-read cDNA sequencing | HGVS notation |
|---|---|---|---|---|---|---|---|
| CF3679 CF6196 | BRCA1 c.4987-1352A > G | Chr 17: 43,069,047 | 0 | P(1); VUS(1) | 1383644 | 17: 43,069,052–43,069,125 | F1662fsX10 |
| CF4358 | BRCA1 c.4358-473T > G | Chr 17: 43,077,087 | 2 | VUS(1) | 3134932 | 17: 43,077,004–43,077,086 | K1452fsX3 |
| CF4455 | BRCA1 c.4986 + 69G > A | Chr 17: 43,070,859 | 0 | none | — | 17: 43,070,863–43,070,927 | F1662fsX13 |
| CF3302 | PALB2 c.3114-239A > T | Chr 16: 23,614,330 | 0 | P(1); VUS(1) | 2156281 | 16: 23,614,332–23,614,492 | W1038X20 |
| CF5431 | ATM c.5763-1080A > G | Chr 11: 108,309,080 | 3 | none | — | 11: 108,308,969–108,309,080 | K1921fsX8 |
| CF6072 | ATM c.5763-1056G > A | Chr 11: 108,309,104 | 0 | LP(2); VUS(1) | 1696413 | 11: 108,308,969–108,309,105 | K1921fsX8 |
| CF6132 | ATM c.8418 + 704G > T | Chr 11: 108,344,075 | 0 | P(1); VUS(1) | 2052386 | 11: 108,342,737–108,342,945 11: 108,343,947–108,344,048 11: 108,342,737–108,342,945 & 11: 108,343,222–108,345,908 |
K2756fsX6 (T1) M2806fsX3 (T2) M2756fsX6 (T3) |
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aThe number of ClinVar entries with this interpretation is given in parentheses; (P) Pathogenic, (LP) likely pathogenic, (VUS) variant of unknown significance. Accessed May 16, 2024.
