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Table 2 Detected pathogenic and likely pathogenic single-nucleotide variants, small indels, and copy number alterations

From: Breast cancer patients suggestive of Li-Fraumeni syndrome: mutational spectrum, candidate genes, and unexplained heredity

Index patient identifier Gene (transcript GRCh37/hg19) Variant type dbSNP Exons/total no. of exons cDNA change Predicted amino acid change Aberration array CGH ACMG class Previously reporteda
7 PALB2 (NM_024675.3) Frameshift rs515726124 4/13 c.509_510delGA p.(Arg170Ilefs*14)   5 Yes
30 RUNX1 (NM_001754.4) Splice donor rs375131372 3/8 c.97+1G>A    4 No
32 ATM (NM_000051.3) Deletion   62–63/63    arr [GRCh37]11q22.3 (108233779_108240057)×1 5 Yes
40 ATM (NM_000051.3) Nonsense   61/63 c.8793T>A p.(Cys2931*)   5 Yes
CHEK2 (NM_007194.3) Deletion   9–10/15    arr [GRCh37]22q12.1 (29092709_29097723)×1 5 Yes
58 CDKN2A (NM_058195.3) Nonsense   2/3 c.292C>T p.(Arg98*)   4 No
RECQL4 (NM_004260.3) Splice donor   7/21 c.1390+1G>C    4 No
59 WRN (NM_000553.4) Deletion   15–16/35    arr [GRCh37]8p12 (30948138_30949422)×1 4 No
60 ATM (NM_000051.3) Nonsense rs587779852 40/63 c.5932G>T p.(Glu1978*)   5 Yes
65 FANCI (NM_001113378.1) Nonsense rs121918164 37/38 c.3853C>T p.(Arg1285*)   5 Yes
PMS2 (NM_000535.5) Deletion   3–8/15    arr [GRCh37]7p22.1 (6035238_6042593)×1 5 No
76 PALB2 (NM_024675.3) Frameshift rs180177143 3/13 c.172_175delTTGT p.(Gln60Argfs*7)   5 Yes
79 RECQL4 (NM_004260.3) Missense and splice region rs186739072 16/22 c.2755G>A p.(Ala919Thr)   4 No
  1. Abbreviations: ACMG American College of Medical Genetics and Genomics, cDNA Complementary DNA, CGH Comparative genomic hybridization, dbSNP Single Nucleotide Polymorphism database
  2. aBased on reports in the literature, ClinVar, Decipher, and gene-specific databases