Spreadsheet: 2e78cba0-78de-4a12-bbff-7612da7c12ac
Sheet: Table S4 BLM variants

Table S4 Variants identified by HRM-based mutation analysis of BLM
 | Sitea | Nucleotide changeb, c | Protein changeb | dbSNP (135) | 1000G MAFd | EVS MAFe | HGMDf | BLM mutation databaseg |  | All BRCAx cases |  | Predictive algorithms
 |  |  |  |  |  |  |  |  |  | Frequency |  | SIFT prediction | PolyPhen-2
Truncating | Ex8 | c.1933C>T | p.(Gln645*) | - | - | 9.295408068414203e-05 | CM973007 | Yes (19) |  | 1/453 (0.22%) |  | - | -
 | Ex14 | c.2695C>T | p.(Arg899*) | - | - | - | CM973010 | Yes (10) |  | 1/453 (0.22%) |  | - | -
Coding non-synonymous | Ex2 | c.11T>C | p.(Val4Ala) | rs144706057 | 0.0005 | 0.001115448968209704 | - | - |  | 4/453 (0.88%) |  | damaging | possibly damaging
 | Ex3 | c.238A>G | p.(Thr80Ala) | - | - | - | - | - |  | 3/453 (0.66%) |  | tolerated | benign
 | Ex3 | c.635C>T | p.(Ser212Phe) | - | - | - | - | - |  | 1/453 (0.22%) |  | damaging | probably damaging
 | Ex4 | c.893C>T | p.(Thr298Met) | rs28384991 | 0.02 | 0.0005578281889178133 | - | - |  | 1/453 (0.22%) |  | tolerated | benign
 | Ex5 | c.968A>G | p.(Lys323Arg) | rs146504061 | - | 0.0003718163227365681 | - | - |  | 1/453 (0.22%) |  | tolerated | probably damaging
 | Ex6 | c.1156A>G | p.(Ile386Val) | - | - | - | - | - |  | 1/453 (0.22%) |  | tolerated | benign
 | Ex8 | c.1928G>A | p.(Arg643His) | rs12720097 | 0.0005 | 0.00408997955010225 | - | - |  | 2/453 (0.44%) |  | tolerated | benign
 | Ex9 | c.2119C>T | p.(Pro707Ser) | rs146077918 | 0.0014 | 0.001487265290946272 | - | - |  | 1/453 (0.22%) |  | tolerated | benign
 | Ex11 | c.2362C>A | p.(Leu788Ile) | - | - | - | - | - |  | 1/453 (0.22%) |  | tolerated | probably damaging
Coding synonymous | Ex3 | c.465T>C | p.(=) | rs185349681 | 0.0014 | 0.0002788622420524261 | - | - |  | 1/453 (0.22%) |  | - | -
 | Ex6 | c.1122T>C | p.(=) | rs28385009 | 0.01 | 0.0005577244841048522 | - | - |  | 1/453 (0.22%) |  | - | -
 | Ex7 | c.1722A>G | p.(=) | rs28385011 | 0.0009 | 0.00408997955010225 | - | - |  | 3/453 (0.66%) |  | - | -
 | Ex10 | c.2268A>G | p.(=) | rs146013879 | 0.0009 | 0.001305483028720627 | - | - |  | 4/453 (0.88%) |  | - | -
 | Ex11 | c.2397T>C | p.(=) | - | - | 9.295408068414203e-05 | - | - |  | 1/453 (0.22%) |  | - | -
Non coding | IVS2 | c.98+33G>T | p.(=) | rs28384975 | 0.0046 | 0.00735020468924451 | - | - |  | 14/453 (3.09%) |  | - | -
 | IVS3 | c.799+7A>G | p.(=) | - | - | - | - | - |  | 1/453 (0.22%) |  | - | -
 | IVS5 | c.1088-40T>C | p.(=) | rs184128669 | 0.01 | - | - | - |  | 1/453 (0.22%) |  | - | -
 | IVS10 | c.2307+53A>G | p.(=) | - | - | - | - | - |  | 1/453 (0.22%) |  | - | -
 | IVS21 | c.4076+4T>G | p.(=) | [NAME] | 0.0027 | 0.003439300985313255 | - | - |  | 8/453 (1.77%) |  | - | -
aExon (Ex), intervening sequence (IVS)
bVariant positions are reported in reference to GenBank reference sequence NM_000057.2  (mRNA)
cIn addition to the variants listed, dbSNPs rs11852361 (c.2603C>T), rs7167216 (c.3961G>A), [NAME] (c.3102G>A), rs2227934 (c.3531C>A), rs1063147 (c.3945C>T), rs28385029 (c.2193+61G>C), rs17181698 (c.2193+84C>T), rs17273206 (c.2308-50G>A), rs3815003 (c.2555+7T>C), rs17273842 (c.3358+32T>G) were detected at high frequency in cases or 1000 Genomes data
dAll variants were queried against 1000 Genomes (1000G) data using the 1000 [NAME] (http://browser.1000genomes.org/index.html) which integrates SNP and indel calls from 1,092 individuals (data release 20110521 v3).  The minor allele frequency (MAF) is provided here.
eAll variants were queried against Exome Variant Server (EVS), NHLBI Exome Sequencing Project (ESP) (http://evs.gs.washington.edu/EVS/) [May 2012].  EVS contains SNP information from 5,379 individuals (data release ESP5400).   The minor allele frequency (MAF) is provided here.
fAll variants were queried against the public version of the Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/)
gAll variants were queried against the BLMbase Mutation Registry (http://bioinf.uta.fi/BLMbase/).  The number in parentheses indicates the number of times this variant has been reported in FA cases