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Table 4 Synonymous variants

From: Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls

Exon Nucleotide changea Protein changea dbSNP ID First reported 1000 G MAFb NHBLI GO ESP MAFc ExACd HAPS cases
(n = 997)e
FCC-ViP cases (n = 999)d Controls
(n = 1998)e
CADD scaled
C score
1 c.12 T > C p.(=) rs145291423 - . . 0.00012 - 1 1 11.2
4 c.768C > T p.(=) rs45487491   . . 0.000037   1   0.3
4 c.1188C > T p.(=) . - . . 0.00003 - - 1 7.6
4 c.1194G > A p.(=) rs61755173 Rahman (2007) [3] 0.0009 0.00154 0.00114 3 2 8 6.4
4 c.1194G > T p.(=) . - . . . 1 - - 6.1
4 c.1242A > C p.(=) . - . . . - - 1 7.7
4 c.1431C > T p.(=) . Teo (2013) . . 0 2 - - 0.0
4 c.1470C > T p.(=) rs45612837 Rahman (2007) [3] 0.0005 0.00015 0.000405 1 - 2 5.8
4 c.1572A > G p.(=) rs45472400 Rahman (2007) [3] 0.0032 0.00339 0.0041 12 12 27 5.6
4 c.1623G > A p.(=) . - . . 0 - 1 2 4.2
5 c.2067G > A p.(=) . Phuah (2013) [38] . 0.00015 0.000018 1 - - 4.1
5 c.2082A > G p.(=) rs150569240 - . . 0.000055 - - 1 5.8
5 c.2091C > A p.(=) . - . . 0 - - 1 4.7
5 c.2244A > G p.(=) . - . . 0.000037 - - 1 5.6
5 c.2328C > T p.(=) rs45508997 - . 0.00008 0 1 - - 4.0
5 c.2337A > C p.(=) . - . . . - 1 - 5.2
5 c.2379C > T p.(=) . - . 0.00008 0.000111 1 1 - 0.1
5 c.2478C > T p.(=) . - . . . - - 1 4.2
5 c.2484C > T p.(=) . - . . . - - 1 6.0
7 c.2742C > T p.(=) rs115759702 - 0.0018 0.00146 0.00003 2 - - 0.7
12 c.3294G > A p.(=) . - . . . - - 1 9.9
12 c.3300 T > G p.(=) rs45516100 Rahman (2007) [3] 0.0183 0.02801 0.0278 64 (1) 68 (4) 123 (1) 7.9
13 c.3495G > A p.(=) rs45439097 Bogdanova (2010) . 0.00108 0.000994 4 7 9 8.6
  1. HAPS Hunter Area Pathology Service, FCC Familial Cancer Centre, ViP Variants in Practice
  2. aVariant positions are reported in reference to NCBI RefSeq NM_024675.3 (mRNA) and NP_078951.2 (protein)
  3. bMinor allele frequency (MAF) reported in the 1000 Genomes (1000 G) cohort Phase 1
  4. cMAF reported in the Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) [46] (data release ESP6500SI-V2)
  5. dMAF reported in ExAC [45] from non-Finnish Europeans, excluding individuals in the database who were part of The Cancer Genome Atlas and therefore known to have had cancer
  6. eNumber of individuals carrying the variant. Where applicable, the number of homozygous carriers is indicated in parentheses