Rare genetic variants included in the iCOGS array.
| Gene | Variant* | Amino acid* | dbSNP rs | Breast cancer risk estimates | Align-GVGD | Reference(s) | Designed‡ | Genotyped | |
|---|---|---|---|---|---|---|---|---|---|
| OR (95% CI) | Penetrance† (95% CI) | ||||||||
| PALB2 | c.1592delT | p.Leu531Cysfs | rs180177102 | 3.94 (1.5-12.1)§ | 40% (17–77) | na | 4, 5, 10 | Yes | Yes |
| c.2323C>T | p.Gln775* | rs180177111 | na | 25, 26 | No | No | |||
| c.2816T>G | p.Leu939Trp | rs45478192 | C55 | 20 | Yes | Yes | |||
| c.3113G>A | p.Trp1038* | rs180177132 | 95% (44–100) | na | 2, 6, 20 | Yes | Yes | ||
| c.3116delA | p.Asn1039Ilefs | rs180177133 | na | 2 | No | No | |||
| c.3549C>G | p.Tyr1183* | rs118203998 | na | 2 | No | No | |||
| CHEK2 | c.349A>G | p.Arg117Gly | rs28909982 | 8.75 (1.06–72.2)¶ | C65 | 11 | Yes | Yes | |
| c.538C>T | p.Arg180Cys | rs77130927 | 2.47 (0.45–13.49)** | C25 | 11 | Yes | Yes | ||
| c.715G>A | p.Glu239Lys | rs121908702 | 1.82 (0.62–5.34)†† | C15 | 11 | Yes | Yes | ||
| c.1036C>T | p.Arg346Cys | na | 8.75 (1.06–72.2)¶ | C65 | 11 | Yes | Yes | ||
| c.1312G>T | p.Asp438Tyr | na | 2.47 (0.45–13.49)** | C25 | 11 | Yes | Yes | ||
| c.1343T>G | p.Ile448Ser | rs17886163 | 1.82 (0.62–5.34)†† | C15 | 11 | Yes | Yes | ||
| ATM | c.7271T>G | p.Val2424Gly | rs28904921 | 52% (28–80) | C65 | 7, 13, 23, 27 | Yes | Yes | |
*Human Genome Variation Society (HGVS); reference sequences PALB2, NM_024675.3, NP_078951.2; CHEK2, NM_007194.3, NP_009125.1; ATM, NM_000051.3, NP_000042.3.
†Age-specific cumulative risk of breast cancer to age 70 years.5–,7
‡Able to be designed for measurement on the custom Illumina iSelect genotyping array.21 ,22
§Breast cancer cases unselected for family history of breast cancer.4
¶OR estimated in a combined group of C65 CHEK2 variants.11
**OR estimated in a combined group of C25 CHEK2 variants.11
††OR estimated in a combined group of C15 CHEK2 variants.11
na, not available.