Table 1

Rare genetic variants included in the iCOGS array.

GeneVariant*Amino acid*dbSNP rsBreast cancer risk estimatesAlign-GVGDReference(s)Designed‡Genotyped
OR (95% CI)Penetrance† (95% CI)
PALB2c.1592delTp.Leu531Cysfsrs1801771023.94 (1.5-12.1)§40% (17–77)na4, 5, 10YesYes
c.2323C>Tp.Gln775*rs180177111na25, 26NoNo
c.3113G>Ap.Trp1038*rs18017713295% (44–100)na2, 6, 20YesYes
CHEK2c.349A>Gp.Arg117Glyrs289099828.75 (1.06–72.2)¶C6511YesYes
c.538C>Tp.Arg180Cysrs771309272.47 (0.45–13.49)**C2511YesYes
c.715G>Ap.Glu239Lysrs1219087021.82 (0.62–5.34)††C1511YesYes
c.1036C>Tp.Arg346Cysna8.75 (1.06–72.2)¶C6511YesYes
c.1312G>Tp.Asp438Tyrna2.47 (0.45–13.49)**C2511YesYes
c.1343T>Gp.Ile448Serrs178861631.82 (0.62–5.34)††C1511YesYes
ATMc.7271T>Gp.Val2424Glyrs2890492152% (28–80)C657, 13, 23, 27YesYes
  • *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.