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HUMAN MUTATION
MUTATION IN BRIEF
HUMAN MUTATION Mutation in Brief 31: E 1200-E1240 (2010) Online
© 2010 WILEY-LISS, INC. DOI: 10.1002/humu.21202
Received 22 April 2009; accepted revised manuscript 17 December 2009.
Characterization of BRCA1 and BRCA2 Deleterious Mutations and Variants of Unknown Clinical Significance in Unilateral and Bilateral Breast Cancer: The WECARE Study Åke Borg1*, Robert W. Haile2, Kathleen E. Malone4, Marinela Capanu3, Ahn Diep2, Therese Törngren1,Sharon Teraoka5, Colin B. Begg3, Duncan C. Thomas2, Patrick Concannon5, Lene Mellemkjaer6, Leslie Bernstein7,Lina Tellhed1, Shanyan Xue2, Eric R. Olson8, Xiaolin Liang3, Jessica Dolle4, Anne-Lise Børresen-Dale9,The WECARE Study Collaborative Group10, and Jonine L. Bernstein3
1Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden; 2Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA; 3Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; 4Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; 5Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; 6Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark; 7Department of Population Sciences, Division of Cancer Etiology, City of Hope National Medical Center, Duarte CA USA; 8Molecular Genetics Program, Benaroya Research Institute, Seattle, WA, USA; 9Departments of Genetics and Medicine, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Norway; 9Faculty division The Norwegian Radium Hospital, Faculty of Medicine, University of Oslo, Norway; 10 WECARE Study Collaborative Group members are listed before references
*Correspondence to: Åke Borg, Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden. Telephone: +46 46 177502; Fax: +46 46 147327; E-mail: [email protected]
Contract grant sponsor: National Cancer Institute, awards CA097397, CA131010 and CA098438.
Communicated by David E. Goldgar
ABSTRACT: BRCA1 and BRCA2 screening in women at high-risk of breast cancer results in the identification of both unambiguously defined deleterious mutations and sequence variants of unknown clinical significance (VUS). We examined a population-based sample of young women with contralateral breast cancer (CBC, n=705) or unilateral breast cancer (UBC, n=1398). We identified 470 unique sequence variants, of which 113 were deleterious mutations. The remaining 357 VUS comprised 185 unique missense changes, 60% were observed only once, while 3% occurred with a frequency of >10%. Deleterious mutations occurred three times more often in women with CBC (15.3%) than in women with UBC (5.2%), whereas combined, VUS were observed in similar frequencies in women with CBC and UBC. A protein alignment algorithm defined 16 rare VUS, occurring at highly conserved residues and/or conferring a considerable biochemical difference, the majority located in the BRCA2 DNA-binding domain. We confirm a multiplicity of BRCA1 and BRCA2 VUS that occur at a wide range of allele frequencies. Although some VUS inflict chemical differences at conserved residues, suggesting a deleterious effect, the majority are not associated with an increased risk of CBC. ©2010 Wiley-Liss, Inc.
KEY WORDS: Breast cancer, BRCA1, BRCA2, contralateral, risk, deleterious mutation, unclassified variants
OFFICIAL JOURNAL
www.hgvs.org
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1201
E 1202 Borg et al.
INTRODUCTION
Women with a BRCA1 (MIM# 113705) or BRCA2 (MIM# 600185) germline mutation are at high risk of developing breast and ovarian cancer (Stratton and Rahman, 2008, Begg et al., 2008). Mutation screening is widely available from health care, research, and commercial laboratories. Thousands of different disease-associated mutations have been identified (Breast Cancer Information Core, BIC). Most deleterious mutations introduce premature termination codons through small frameshift deletions or insertions, nonsense or splice junction alterations, or large deletions or duplications. Some splice site mutations and large rearrangements do not change the reading frame, but result in a loss or gain of one to several exons, which is thought to compromise the gene function. Deleterious missense mutations are typically confined within specific residues of functional motifs. However, the risk contribution of numerous other sequence variants remains unclear. These ‘variants of unknown significance’ (VUS) include missense changes and small in-frame deletions and insertions, coding synonymous nucleotide substitutions that do not lead to amino acid shifts, as well as alterations in non-coding intervening sequences (IVS) or in untranslated exonic regions (UTRs).
Classifying VUS remains a great challenge for designing tailored genetic counseling and disease prevention strategies. First, VUS greatly outnumber known deleterious mutations and include both unidentified deleterious mutations as well as neutral variants with no clinical importance. As individual VUS are rare, the usual genetic approach of linkage/segregation or association analysis typically used to classify sequence variants is difficult to apply. As homozygosity or compound heterozygosity for deleterious mutations are embryonically lethal or associated with severe syndromes, VUS that co-occur with a known disease-associated mutation in trans can be classified as not being high-risk alleles. However, this approach relies on the correct determination of allelic phases (Judkins et al., 2005; Tavtigian et al., 2006). A variety of functional assays have been developed for BRCA1 including transcription activation small colony phenotype rescue of radiation resistance and ubiquitin ligase activity; and for BRCA2, assays for homologous recombination, crosslink dependent survival, centrosome amplification or rescue of mouse embryonic stem cell viability (Carvalho et al., 2007; Kuznetsov et al., 2008). Although potentially excellent strategies, they are mostly restricted to variants of certain domains and require laborious optimization. In the absence of a universal functional assay, in silico predictions of missense variants by assessment of phylogenetic conservation and severity in modification of biophysical characteristics of amino acids have also been utilized (Abkevich et al., 2004; Tavtigian et al., 2006). Moreover, all coding sequence alterations, including synonymous variants, can be assessed for potential to disrupt exonic splicing enhancer and silencer elements, or introduce cryptic splice sites, and should be considered along with variants in the exon/intron splice junction consensus sites as potentially affecting transcript processing. Multifactorial likelihood-ratio models have been developed to integrate information from these various sources, including tumor histopathological characteristics, providing likelihood ratios for or against disease causality for a considerable number of VUS (Goldgar et al., 2004; Chenevix-Trench et al., 2006; Easton et al., 2007). Nevertheless, the majority of variants studied remain of unknown clinical importance.
The Women’s Environment, Cancer, and Radiation Epidemiology (WECARE) Study was established to examine the combined roles of postoperative radiation exposure and genetic susceptibility in the etiology of contralateral breast cancer (CBC). A large multi-center, population-based series of asynchronous CBC and a reference group of matched unilateral breast cancer (UBC) was designed (Bernstein et al., 2004). We previously reported results from this series regarding estimates of risk variation in carriers of deleterious BRCA gene mutations (Begg et al., 2008). In the present study, we report results on the frequency and pattern of all types of BRCA1 and BRCA2 sequence variants. We used in silico analysis to predict the functional consequence of missense variants and CBC-UBC comparisons of groupings of variants to explore their association with breast cancer risk.
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1203
MATERIALS AND METHODS
Study population The WECARE Study population included 705 women with CBC and 1398 women with UBC who were
ascertained through five population-based cancer registries. Controls (women with UBC) were individually matched to the cases (women with CBC) on age, date of diagnosis, race, and registry (Bernstein et al., 2004). All were diagnosed with their first primary breast cancer at age 54 years or younger (mean age 46 years) and the mean interval from first to second breast cancer in the CBC group was 5 years (range 1-16 years). UBC controls were also counter-matched on radiation treatment (Bernstein et al., 2004). The proportion of women of Jewish ancestry was similar by CBC-UBC status (7.7%). A first-degree (affected mother, sister or daughter) family history of breast cancer was reported more frequently in women with CBC (32%) than in women with UBC (21%).
BRCA gene analysis and quality controls The complete coding sequences of BRCA1 and BRCA2 were screened for variations by denaturing high-
performance liquid chromatography (DHPLC) and sequence analysis, including a stepwise laboratory quality control (QC) scheme as previously described (Begg et al., 2008). In total, 139 samples were tested in the inter-lab QC step. Of the 9,869 fragments tested, discrepant results were observed for 52 (0.53%) of the fragments. For the intra-lab QC, of the 21,158 fragments tested, from 298 samples, discrepant results were observed for 111 (0.52%) fragments. In terms of the consistency of classifying deleterious mutation carrier status, among the 298 women whose specimens were tested twice within the same screening laboratory, only two (0.67%) had discrepant results, and among the 139 women whose samples were re-screened by the centralized laboratory, three (2.16%) had discrepant results. When QC results were un-blinded, discrepant results were resolved.
Sequence variation nomenclature All sequence variants were named and are referred to in the text according to the nomenclature used by Human
Genome Variation Society (HGVS) (http://www.hgvs.org) recommendation guidelines, using the A of the ATG-translation initiation codon as nucleotide +1 (den Dunnen and Antonarakis, 2000). Mutations are also provided using the BIC (http://research.nhgri.nih.gov/bic) nomenclature, with nucleotide numbering starting at the first transcribed base of BRCA1 (GenBank U14680.1) and BRCA2 (NM_000059.1). In Supp. Tables S1 and S2, all sequence variants are listed according to both BIC and HGVS.
In silico analyses BRCA missense variants were analyzed using web-based algorithms, using information that is entirely external
to the WECARE Study data. Align-GVGD (http://agvgd.iarc.fr/) combines the biophysical characteristics (side-chain composition, polarity and volume) of amino acids and protein multiple sequence alignments (Grantham Variation (GV) and Grantham Deviation (GD) scores) to predict where amino acid substitutions fall in a spectrum from enriched deleterious to enriched neutral, providing GV and GD scores (0 to >200) and graded classifiers (C0 to C65) (Tavtigian et al., 2006). Alignments were done with up to 13 BRCA1 sequences and 12 BRCA2 sequences to the depth of Xenopus laevis (frog), Tetraodon nigroviridis (pufferfish - green spotted) or Strongylocentrotus purpuratus (purple sea urchin).
Definition of deleterious mutations Sequence variants were categorized based on their predicted effect on the mRNA and amino acid level and
defined as deleterious mutations according to the following established (BIC) criteria: (1) all frameshift and nonsense variants with the exception of the neutral stop codon BRCA2 c.9976A>T (BIC: K3326X) (Mazoyer et al., 1996), and other variants located 3’ thereof; (2) all IVS variants occurring in the consensus splice acceptor or donor sequence sites, either within 2 bp of exon-intron junctions or when experimentally demonstrated to result in abnormal mRNA transcript processing; (3) missense variants that have been conclusively demonstrated, on the
E 1204 Borg et al.
basis of data from linkage analysis of high risk families, functional assays or biochemical evidence, to have a deleterious effect on known functional regions. In this study, all variants not previously identified as being deleterious by these criteria were considered “VUS”.
Statistical Analyses Age-adjusted conditional logistic regression was used to estimate the relative risks (RR) and corresponding
95% confidence intervals (95% CI) of common VUS as well as of rare variants grouped by type (deleterious, missense VUS, synonymous VUS, IVS VUS). Models included an “offset” term to account for the counter-matching. All analyses were conducted using SAS TPHREG (SAS Institute, Cary, NC).
RESULTS
Deleterious mutations identified The mutation screening of 2103 participants (705 CBC and 1398 UBC) resulted in the discovery of 113 unique
deleterious mutations, 57 in BRCA1 and 56 in BRCA2 (Figure 1, Supp. Table S1). These variants, and the corresponding familial aggregations of breast cancer in their relatives, were used in an earlier article to calculate penetrance estimators (Begg et al., 2008). The variants included 73 small frameshift deletions or insertions, 26 nonsense mutations, 7 missense and 7 splice site mutations. Five of the 7 deleterious splice site mutations were located within 2 bp from the exon/intron boundaries. BRCA2 c.9501+3A>T (BIC: IVS25+3A>T) was classified as deleterious because segregation/clinical data are supportive and cDNA analysis confirms aberrant transcript splicing, i.e. exon 25 skipping, resulting in a frameshift and an almost immediate premature stop codon. BRCA1 c.211A>G (BIC: R71G) is located in exon 5, two nucleotides from the 3´-exon/intron junction, and shown to introduce an aberrant cryptic splice site (Vega et al., 2001). All 7 splice site mutations were predicted to give rise to out-of-frame transcripts leading to premature stop codons. The 7 missense mutations defined as deleterious included BRCA1 c.130T>A (BIC: C44S) and c.181T>G (BIC: C61G), both occurring at zinc-ligating residues in the RING domain (Morris et al., 2006), and repeatedly found to segregate with disease in breast-ovarian cancer families in Scandinavia or globally. BRCA1 c.5095C>T (BIC: R1699W), c.5123C>A (BIC: A1708E), c.5213G>A (BIC: G1738E) and c.5324T>G (BIC: M1775R) all affect structurally and functionally critical residues in the BRCT domains and are mutations described previously in breast cancer families (Vallon-Christersson et al., 2001; Olopade et al., 2003; Williams et al., 2003). BRCA2 c.3G>A (BIC: M1I) disrupts the translation initiation codon and was classified as deleterious since a possible re-initiation at Met-124 would result in an amino-terminal truncated protein lacking important regulatory regions (Xia et al., 2006). Finally, three sequence variants – BRCA2c.9976A>T (BIC: K3326X), c.10095delCins11 (BIC: 10323delCins11) and c.10150C>T (BIC: R3384X) – predicted to result in protein truncation were ruled as exceptions that could not be classified because of their location near the 3´-end and possibly dispensable part of the gene. Thus, the most carboxy-terminal deleterious mutation in BRCA2 was c.9541_9554del14 (BIC: 9769del14) and c.5558dupA (BIC: 5677insA) in BRCA1, the latter predicted to result in a protein truncated by only the last 11 amino acids. Our approach to classifying mutations as deleterious follows the approach currently used in oncogenetic clinics and is compatible with classifications in the BIC. Our screening method did not target larger genomic deletions or duplications. Thus, it is possible that some deleterious mutations may have been missed.
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1205
Figure 1. Spectrum of deleterious BRCA1 (n=57) and BRCA2 (n=56) mutations detected in 705 women with CBC (red) and 1398 women with UBC (yellow), displayed by gene 5’ to 3’ location and number of observations. Mutation nomenclature according to BIC.
Frequency of deleterious mutations in women with CBC and UBC A total of 181 (8.6%) of 2103 participants were found to carry one of the 113 unique deleterious BRCA
mutations (Figure 1, Supp. Table S1). No woman carried more than one deleterious mutation. Mutations were more common in BRCA1 (n=109) than in BRCA2 (n=72). Multiple women carried known founder mutations such as BRCA1 c.68_69delAG (BIC: 185delAG) (n=16), c.181T>G (BIC: C61G) (n=10), c.5266dupC (BIC: 5382insC) (n=10), and BRCA2 c.5946delT (BIC: 6174delT) (n=5) and c.2808_2811delACAA (BIC: 3036del4) (n=5). Eighty-nine of the 113 mutations were detected only once (Figure 1). Deleterious mutations were nearly three times more common in women with CBC (15.3%) than in women with UBC (5.2%). Carrying a mutation in either BRCA1 or BRCA2 was associated with a 4-fold increased risk of CBC (95% CI 2.8-5.7) as compared to not having a deleterious mutation (Table 1). BRCA1 mutation carriers had a 4.5-fold increased risk (95% CI 2.8-7.1) and carriers of a BRCA2 mutation had a 3.4-fold increased risk (95% CI 2.0-5.8) of CBC. The increased risk of CBC was evident irrespective of mutation type, i.e. frameshift, nonsense, splice site or missense mutation (Table 1) (Malone et al., submitted 2009).
Effect of position of deleterious mutations
A lower frequency of CBC patients with mutations located in the 3´ part of BRCA1 as compared with the 5´ and middle-region of BRCA1 was noted (Figure 1). The RR of CBC in the 13 women carrying the most 3´ located truncating mutations (here including c.5266dupC (BIC: 5382insC), c.5444G>A (BIC: W1815X), c.5503C>T (BIC: R1835X) and c.5558dupA (BIC: 5677insA)) was 0.7, while the RR was 5.3 in the 80 women carrying any other truncating BRCA1 mutation (Table 1). No such effect for corresponding 3´ located truncating BRCA2 mutations remained after excluding c.9976A>T (BIC: K3326X), c.10095delCins11 (BIC: 10323delCins11) and c.10150C>T (BIC: R3384X). There was no significant difference regarding the risk of CBC in women with
E 1206 Borg et al.
premature stop codons occurring within or outside (either N- or C-terminal) the ‘ovarian cancer-cluster region’ (OCCR, nucleotides 3059-6629; GenBank NM_000059.1) of BRCA2 (Table 1) (Gayther et al., 1997).
Table 1. Risk of CBC compared to UBC, in relation to known deleterious mutations in BRCA1 and BRCA2. CBCa UBCa Carrier Status N % N % Adjb % RRc 95% CI No known deleterious mutation in BRCA1/2 d 597 84.7 1325 94.8 95.1 1.0 Ref. Deleterious mutation in BRCA1 or BRCA2 108 15.3 73 5.2 4.9 4.0 2.8-5.7 Deleterious mutation in BRCA1 67 9.5 42 3.0 2.6 4.5 2.8-7.1 Deleterious mutation in BRCA2 41 5.8 31 2.2 2.4 3.4 2.0-5.8 Frameshift, nonsense, splice mutation in BRCA1 56 7.9 37 2.6 2.4 4.2 2.5-7.0 Deleterious missense mutation in BRCA1 11 1.6 5 0.4 0.2 6.3 2.0-19.9 Frameshift, nonsense, splice mutation in BRCA2 41 5.8 30 2.1 2.3 3.6 2.1-6.1 Deleterious missense mutation in BRCA2 0 0 1 0.1 0.1 - - BRCA1, 3´end mutations e 3 0.4 10 0.7 0.5 0.7 0.2-3.2 BRCA1, all other truncating mutations 53 7.5 27 1.9 1.8 5.3 3.0-9.3 BRCA2, OCCR mutations f 11 1.6 11 1.1 1.1 3.2 1.3-8.0 BRCA2, all other deleterious truncating mutation 30 4.3 19 1.1 1.2 3.8 1.9-7.3
a Women with UBC (N=1398) served as reference group for women with CBC (N=705). b UBC proportions computed as if UBCs were randomly selected. c Relative risk was adjusted for counter-matching and age at first primary; 95%CI: 95% confidence interval. d Wildtype and all variants of unknown significance that have not earlier been classified as deleterious (see Supp. Table S2). e 5382insC, W1815X, R1835X and 5677insA of BRCA1 (GenBank U14680.1), nomenclature according to BIC. f OCCR (Ovarian Cancer Cluster Region) premature stop codon occurring within nt. 3059-6629 of BRCA2 (GenBank NM_000059.1). Mutation nomenclature according to HGVS is found in Supp. Table S1.
Classification of VUS Screening of 2103 women resulted in the identification of an additional 357 unique sequence variants that were
not classified as deleterious (complete list in Supp. Table S2). These 357 variants, including both VUS and suspected (BIC) neutral variants, were broadly categorized according to type into: non-synonymous (n=185), synonymous (n=69), and IVS alterations (n=91). The results from these 345 variants are summarized in Tables 2a and 2b. In addition we found 4 rare in-frame deletions, 5 variants in UTRs, 1 neutral frameshift (BRCA2 c.10095delCins11 (BIC: 10323delCins11)) and 2 neutral nonsense (BRCA2 c.9976A>T (BIC: K3326X) and c.10150C>T (BIC: R3384X)) variants. The majority (n=210) of the 357 variants were observed only once while 81 other variants had a minor allele frequency (MAF) less than 0.1% (observed 4 times or less among the 4206 alleles). In contrast there were 16 common variants with MAF>10%. A substantial number (n=133) of variants found once or a few times have not been reported earlier (in BIC) (highlighted in blue in Supp. Table S2). This observation should, however, be interpreted cautiously since VUS are probably less frequently reported and are likely under-represented in public databases. Interestingly, the numbers of coding variants found in the BRCA genes are high considering that the average gene contains only a handful (~4) of coding SNPs with an allele frequency of at least a few percent in the population. Typically, non-synonymous SNPs not only occur less often but also have lower MAF, often less than 5% (Cargill et al., 1999).
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1207
Table 2a. MAF of BRCA1 sequence VUSa, identified in women with CBC or UBC.
Typeb MAF CBC UBC Relative Risk (95% CI) c,d
Missense 53 unique variants <0.1% 21 46 1.0 (0.6-1.7) 4 unique variants 0.1-0.5% 9 35 0.6 (0.3-1.2) 2 unique variants 0.5-2.5% 42 81 1.1 (0.8-1.7) Q356R 6.0% 65 165 0.8 (0.6-1.2) D693N 7.1% 87 180 1.1 (0.8-1.4) E1038G 25% 271 646 0.9 (0.7-1.0) K1183R 26% 272 642 0.9 (0.7-1.1) P871L 26% 278 668 0.8 (0.7-1.0) S1613G 29% 291 693 0.8 (0.7-1.0)
Synonymous 13 unique variants <0.1% 4 15 0.6 (0.2-1.7) 2 unique variants 0.1-0.5% 2 9 0.5 (0.1-2.2) no variant 0.5-2.5% - - - L771L 25% 268 640 0.8 (0.7-1.0) S1436S 26% 269 653 0.8 (0.7-1.0) S694S 28% 278 676 0.8 (0.7-1.0) IVS 32 unique variants <0.1% 11 21 1.4 (0.6-3.0) 4 unique variants 0.1-0.5% 10 19 1.2 (0.6-2.7) no variant 0.5-2.5% - - - IVS17-53C>T 2.7% 24 77 0.7 (0.4-1.1) IVS7-34C>T 19% 222 495 1.0 (0.8-1.2) IVS8-58delT 28% 285 672 0.9 (0.7-1.1) IVS7+36del14 33% 314 745 0.8 (0.7-1.0)
a Individuals with rare variants are aggregated within MAF categories. Common variants (MAF>2.5%) are listed separately. Frequencies correspond to combined frequencies of heterozygotes or homozygote variants. b In addition to the variant types listed, 2 women with CBC and 7 women with UBC had rare variants that were either in-frame deletions or variants in the untranslated regions. BRCA1 (GenBank U14680.1) mutation nomenclature according to BIC. IVS=intervening sequence (noncoding). Mutation nomenclature according to HGVS is found in Supp. Table S1. c 95% confidence interval. d The reference group for each RR consists of women carrying all other types of VUSs and excludes carriers of known deleterious BRCA mutations.
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Table 2b. MAF of BRCA2 sequence VUSa, identified in women with CBC or UBC. Typeb MAF CBC UBC Relative Risk (95%CI) c,d
Missense 102 unique variants <0.1% 46 72 1.4 (0.9-2.0) 10 unique variants 0.1-0.5% 24 57 0.9 (0.5-1.5) 4 unique variants 0.5-2.5% 22 64 0.7 (0.4-1.2) T1915M 2.6% 26 74 0.8 (0.5-1.2) N289H 3.5% 44 92 1.1 (0.7-1.6) N991D 3.5% 43 92 1.0 (0.7-1.5) N372H 28% 310 627 1.2 (1.0-1.4) Synonymous 40 unique variants <0.1% 18 34 1.2 (0.7-2.2) 6 unique variants 0.1-0.5% 19 37 1.1 (0.6-2.0) no variant 0.5-2.5% - - - H743H 3.4% 42 90 1.0 (0.7-1.5) S455S 3.5% 44 89 1.1 (0.7-1.6) V1269V 16% 177 419 0.9 (0.7-1.1) S2414S 19% 207 477 1.0 (0.8-1.2) K1132K 23% 267 581 1.1 (0.9-1.3) IVS 41 unique variants <0.1% 20 33 1.4 (0.8-2.5) 8 unique variants 0.1-0.5% 20 48 0.9 (0.5-1.6) 1 unique variants 0.5-2.5% 8 23 0.7 (0.3-1.6) IVS16-14T>C 28% 325 689 1.1 (0.9-1.3)
a Individuals with rare variants are aggregated within MAF categories. Common variants (MAF>2.5%) are listed separately. Frequencies correspond to combined frequencies of heterozygotes or homozygote variants. b In addition to the variants listed, 3 women with CBC and 3 women with UBC had rare variants that were either in-frame deletions, frameshifts, nonsense mutations or variants in the untranslated regions (UTR). In addition there is a 5’ UTR polymorphism (203G>A) that was observed in 269 CBC and 528 UBC (OR=1.0). BRCA2 (GenBank NM_000059.1) mutation nomenclature according to BIC. IVS=intervening sequence (noncoding). Mutation nomenclature according to HGVS is found in Supp. Table S1. c 95% confidence interval. d The reference group for each RR consists of women carrying all other types of VUSs and excludes carriers of known deleterious BRCA mutations.
Frequency of VUS in women with CBC and UBC Combined, rare VUS occurred in similar proportions in women with CBC and UBC (Tables 2a and 2b).
Broadly, VUS, regardless of their MAFs’, occurred in similar frequencies in women with CBC and UBC for both BRCA1 variants (Table 2a) and BRCA2 variants (Table 2b). In these tables, rare variants have been grouped according to both type and MAF, while more common variants (MAF>2.5%) are listed individually. None of the sub-groups demonstrate a statistically significant effect on risk of CBC. Since these comparisons aggregate many individual variants we cannot on this basis rule out the possibility that there are a few rare variants that are actually associated with risk.
BRCA1 has four very common missense variants (c.2612C>T (BIC: P871L), c.3113A>G (BIC: E1038G), c.3548A>G (BIC: K1183R), c.4837A>G (BIC: S1613G)) with MAF>20%, and another two (c.1067A>G (BIC: Q356R and c.2077G>A (BIC: D693N)) with MAFs of 6% and 7% respectively. In BRCA2, one missense variant
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1209
(c.1114A>C (BIC: N372H)) has a MAF>20% and three others (c.865A>C (BIC: N289H), c.2971A>G (BIC: N991D) and c.5744C>T (BIC: T1915M)) have MAFs of 2-4%. It is expected that these 10 are neutral variants of negligible functional and clinical significance. The observed relative frequencies of these variants in CBC versus UBC are consistent with the hypothesis that these variants do not affect the risk of breast cancer. However, homozygous status for BRCA2 His372 has previously been associated with a slight increased risk of breast cancer (Healey et al., 2000). We saw no statistically significant increased risk of CBC in homozygous or heterozygous His-372 carriers as compared to WT (RR for heterozygous 1.19 95%CI: 0.97-1.47, and RR for homozygous 1.12 95%CI: 0.77-1.63).
Functional assessment of non-synonymous VUS We used Align-GVGD to further assess the functional effect of missense variants, with alignment to 13 BRCA1
and 12 BRCA2 ortholog sequences down to sea urchin. Six VUS (BRCA1 c.2596C>T (BIC: R866C), BRCA2 c.4585G>A (BIC: G1529R), c.7878G>C (BIC: W2626C), c.7988A>T (BIC: E2663V), c.7994A>G (BIC: D2665G) and c.9154C>T (BIC: R3052W)) occurred at strongly conserved residues (GV=0) and had a GD�65. Thus, these were inferred to belong to the class (C65) of substitutions most likely to interfere with function and were in this respect comparable to five of the missense mutations a priori classified as deleterious (the remaining, BRCA1 c.5324T>G (BIC: M1775R) had a GV=14.30 and was inferred to class C45, while BRCA2 c.3G>A (BIC: M1I) had a GV=0 but GD as low as 10.12). Two other BRCA2 variants (c.9104A>G (BIC: Y3035C) and c.10045A>G (BIC: T3349A)) were defined as interfering with function (A-GVGD class C55), an additional 8 VUS had either a low GV or high GD score which lifted them above class C0 and the remaining 169 amino acid substitutions were less likely to compromise function. Details of 16 variants are presented in Table 3 with corresponding details of all VUS missense variants in Supp. Table S3. Lowering the sequence alignment stringency to the level of pufferfish and frog, respectively, led to another 7 and 16 VUS predicted to be functionally defective (C15-C55, Supp. Table S3).
All 8VUS with the highest likelihood of being deleterious (A-GVGD class C55-C65 in alignment down to sea urchin) were rare (found once or twice), while another 8VUS reaching class C15-C35 in alignment to sea urchin were observed a total of 18 times. However, the aggregated ratio of CBC (11) to UBC (18) only slightly exceeds the reference ratio of one CBC to every two UBCs in the study. The 15 VUS assigned to class C15-C65 in alignments to pufferfish or frog, but to C0 in alignment to sea urchin, were observed 78 times. The latter group included BRCA1 c.134A>C (BIC: K45T) in the RING domain (see below), as well as BRCA2 c.8851G>A (BIC: A2951T) (class C55), which was observed 22 times and had an elevated frequency in women with CBC (10 CBC versus 12 UBC). Interestingly, this variant has earlier been suggested as a moderate-risk predisposing allele (Hammet et al., 2008).
Functional domains affected by non-synonymous VUS None of the missense or in frame deletion variants identified in the present study affected the numerous putative
phosphorylation sites in BRCA1 or BRCA2, nor were they found in the nuclear localization signals of BRCA1 (amino acids 503-508 and 606-615) nor of BRCA2 (amino acids 3266-3269 and 3311-3315). Besides the two deleterious mutations at Cys44 and Cys61, a third variant (c.134A>C (BIC: K45T), observed once) affected the BRCA1 RING domain (amino acids 1-100). Although not as strongly conserved as the RING domain cysteine residues, Lys45 is part of a beta-sheet and K45T disrupts a salt bridge to Glu75, likely to weaken the folding and interaction with the E2 ubiquitin-conjugating enzyme UbcH5a (Morris et al., 2006). Several known deleterious missense mutations were found in the BRCA1 carboxy terminal region including the two BRCT domains (amino acids 1625-1825), but only one (c.5401G>T (BIC: G1801C)) of five other missense VUS in this region had an A-GVGD score suggesting a possible functional interference. The majority of BRCA2 VUS with an A-GVGD score suggesting a deleterious effect were located in the DNA binding domain (amino acids 2500-3098). Moreover, c.4585G>A (BIC: G1529R) affects a highly conserved residue in the Rad51 binding BRC4 motif of BRCA2 (Bignell et al., 1997). BRCA1 c.2596C>T (BIC: R866C) is located in a highly conserved region ‘motif 6’, still of unknown function, while BRCA1 c.4172T>C (BIC: I1391T) affects the coiled coil region (Abkevich et al., 2004).
E 1210 Borg et al.
Table 3. (a) BRCA1 and BRCA2 VUS identified in CBC and UBC as potentially deleterious by A-GVGD protein alignment algorithm (to the depth of Sea Urchin), yielding a GV=0 and/or a GD�65. (b) A-GVGD scores, CBC and UBC numbers of BRCA1 and BRCA2 missense variants earlier classified as being deleterious mutations. (a) A-GVGD Gene Exon NTa Base Ch BICb Class GV GD CBC UBC BRCA1 7 433 A>G Y105C c,d C15 120 131 0 1 BRCA1 8 655 A>G Y179C C35 40 182 0 2 BRCA1 11 2640 C>T R841W C15 111 78 2 6 BRCA1 11 2715 C>T R866C c,d C65 0 180 0 1 BRCA1 12 4291 T>C I1391T C25 30 70 1 0 BRCA1 22 5520 G>T G1801C C15 157 107 0 1 BRCA2 11 4813 G>A G1529R c,d C65 0 125 2 0 BRCA2 17 8106 G>C W2626C C65 0 214 1 0 BRCA2 17 8107 A>T I2627F C15 0 21 0 1 BRCA2 18 8216 A>T E2663V C65 0 121 0 1 BRCA2 18 8222 A>G D2665G c,d C65 0 94 1 1 BRCA2 18 8267 A>G D2680G C15 44 75 0 1 BRCA2 22 9078 G>T K2950N d C35 26 79 3 0 BRCA2 23 9332 A>G Y3035C C55 21 192 1 1 BRCA2 24 9382 C>T R3052W C65 0 101 0 1 BRCA2 27 10273 A>G T3349A c,d C55 0 58 0 1 Total 11 18 (b) BRCA1 3 249 T>A C44S e C65 0 112 2 0 BRCA1 5 300 T>G C61G e C65 0 158 8 2 BRCA1 18 5214 C>T R1699W e C65 0 101 0 1 BRCA1 18 5242 C>A A1708E e C65 0 107 1 0 BRCA1 20 5332 G>A G1738E e C65 0 98 0 1 BRCA1 21 5443 T>G M1775R e C45 14 91 0 1 BRCA2 2 231 G>A M1I e C0 0 10 0 1 Total 11 6 a NT: nucleotide. BRCA1 (GenBank U14680.1), BRCA2 (GenBank NM_000059.1), according to BIC. b BIC: nomenclature according to Breast Cancer Information Core (see Supp. Table S2 for HGV nomenclature). c Classified as of no clinical interest in BIC. d Classified as neutral in the likelihood-ratio model developed by Easton et al. (2007). e BRCA1 and BRCA2 missense variants a priori classified as deleterious mutations in the present study.
DISCUSSION
Predisposition to breast cancer can be attributed to several levels of genetic susceptibility: rare high-risk alleles, rare moderate-risk alleles and common low-risk alleles (Stratton and Rahman, 2008). Deleterious mutations in BRCA1 and BRCA2 account for a considerable proportion of dominantly inherited breast cancer and have received wide acceptance in diagnostic testing and prevention. BRCA1 and BRCA2 mutation screening results in the identification of sequence variants that cannot be unequivocally referred to as deleterious or neutral. This is emphasized by the results from the present study of a high-risk population of young (<55 years) women with breast cancer. Using a carefully optimized DHPLC screening approach to analyze all coding exons and flanking intronic regions of BRCA1 and BRCA2, we identified 470 unique sequence variants in 2103 women. The majority (n=299) of variants were observed only once, however, there were some that were very common (MAF>10%).
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1211
Based on documented knowledge on effects of variants that give rise to premature stop codons (via frameshift insertions or deletions, nonsense or consensus splice site sequence changes) or missense alterations at critical residues in functional domains, we defined 113 unique BRCA1 or BRCA2 variants as deleterious mutations. These were observed in 181 (8.6%) of the 2103 women. We confirmed earlier observations (BIC; Thomassen et al., 2008), of global or local founder effects for certain recurrent mutations and also describe a set of unique mutations as previously reported (Begg et al., 2008; Malone et al., submitted 2009). Deleterious mutations were three times as common in women with CBC (15.3%) than in women with UBC (5.2%), and carrying a deleterious mutation in either BRCA1 or BRCA2 conferred an approximately 4-fold increased risk of CBC among survivors of a first breast cancer (Begg et al., 2008; Malone et al., submitted 2009).
Previous studies have suggested a genotype-phenotype correlation within BRCA1 in which women with truncating mutations 3´ of the exon 12/13 boundary show a significantly decreased ovarian to breast cancer ratio (Gayther et al., 1995; Holt et al., 1996; Thompson et al., 2002). Our study design precluded assessment of the breast-ovarian cancer mutation location question but allowed us to assess whether the occurrence of CBC was related to location. We observed a lower frequency of CBC patients with mutations located in the 3´ part of BRCA1 as compared with the 5´ and middle-region of BRCA1. This was an unexpected finding considering that most transcripts with premature termination codons are targeted for degradation by the nonsense-mediated mRNA decay (NMD) surveillance pathway, resulting in no or low expression of nonsense transcripts and truncated protein products (Perrin-Vidoz et al., 2002; Conti and Izaurralde, 2005). However, transcripts bearing termination codons located <50 nucleotides from the last exon-exon junction (EEJ) or lacking a downstream EEJ (i.e., premature stop codons occurring in the last exon) may escape NMD. Thus, transcripts with premature stop codons occurring at BRCA1 codon 1807 or later may be translated and partly functional. Indeed, decreased but detectable expression of mutant protein has been found in HCC1937 cells carrying the BRCA1 5382insC mutation (Scully et al., 1999). However, despite the noted differences in the frequencies of women with CBC and UBC in the 5´ and 3´ parts of BRCA1, the numbers are small and results must be carefully interpreted. Truncating mutations in a central region of BRCA2 have been associated with an increased risk of developing ovarian cancer relative to breast cancer as compared to mutations occurring outside this OCCR bounds (Gayther et al., 1997; Thompson et al., 2001). It is less likely that escape from the NMD pathway explains this BRCA2 genotype-phenotype correlation (Ware et al., 2006), and we detected only a small, non-significant difference in the incidence of CBC in women with truncating mutations in a region overlapping with the OCCR. However, it cannot be excluded that expression of truncated BRCA proteins in variable degree interferes with normal BRCA function in tumorigenesis or retains some functions that influence tumor biology and DNA damage control in response to therapy in the absence of wildtype BRCA protein.
An even more complicated circumstance concerns the significance of expression of full-length BRCA proteins with missense mutations or small in-frame amino acid deletions/insertions. We identified seven missense variants that have been previously unambiguously defined as high-risk alleles due to known interference with function or translation initiation, or based on segregation analysis in affected families. These deleterious mutations were located at residues in the BRCA1 RING domain, important for ubiquitin-ligase activity, or in the BRCA1 BRCT-domains that interact with numerous proteins involved in transcription and DNA repair. However, we identified an additional 185 unique missense variants (and four in-frame single amino acid deletions) that could not straightforwardly be classified as risk-alleles. Again, the majority of these types of variants were rare and occurred in single individuals, while the minority were common. While it might be argued that the common variants are unlikely to be functional and should be referred to as neutral variants or polymorphisms, there is some suggestion that common BRCA missense variants may have a role as low-risk alleles (Healey et al., 2000; Hammet et al., 2008). We saw no evidence for increased risk associated with any of the common missense variants.
Theoretically, to further examine the role of each missense variant, one could take into account the multiplicity of functions and regions in both BRCA1 and BRCA2 that are involved in protein or DNA binding or constitute sites for enzymatic modification; however, the limited number of individual variants and lack of experimental validation would make such comparisons speculative and inconclusive. Therefore, we used publicly available protein alignment algorithms to more objectively evaluate the possible consequence of each amino acid substitution. Using Align-GVGD, we identified a set of 16 missense VUS (Table 3) that occurred at highly conserved (Grantham Variation=0) residues or conferred a considerable biochemical difference (Grantham Deviation�65). Six of these occurred in BRCA1 and regions of unclear function such as the highly conserved motif 6 (Arg-866) or the coiled coil region (Ile-1391) (Abkevich et al., 2004), while ten were found in BRCA2.
E 1212 Borg et al.
Interestingly, the majority (8/10) of the latter were located in the BRCA2 DNA binding domain (amino acids 2500-3098), an observation also made by others (Wu et al., 2005; Easton et al., 2007).
It is notable that the relative frequencies of CBC and UBC among the 16 VUS suggested by A-GVGD as candidate risk variants show no collective evidence of increased breast cancer risk (11/29 (38%) CBC, as compared with 705/1398 (34%) in the entire study). Furthermore, four (BRCA1 c.314A>G (BIC: Y105C), c.2596C>T (BIC: R866C), BRCA2 c.4585G>A (BIC: G1529R) and c.7994A>G (BIC: D2665G)) of the 16 VUS suggested by A-GVGD as candidate risk variants have been reported in BIC as of no clinical interest primarily based on co-occurrence (also in trans) with deleterious mutations and lack of segregation with disease in families, and six (BRCA1 c.314A>G (BIC: Y105C), c.2596C>T (BIC: R866C), BRCA2 c.4585G>A (BIC: G1529R), c.7994A>G (BIC: D2665G), c.8850G>T (BIC: K2950N) and c.10045A>G (BIC: T3349A)) were also classified as neutral in the likelihood-ratio model developed by Easton et al. (2007). However, two VUS scored as possibly deleterious were in agreement with Easton et al. (2007) (BRCA2 c.7878G>C (BIC: W2626C) and c.7988A>T (BIC: E2663V)) and two (BRCA2 c.7988A>T (BIC: E2663V) and c.9154C>T (BIC: R3052W)) were confirmed as deleterious in a recent study using a mouse embryonic stem cell assay (Kuznetsov et al., 2008). Thus, there is little evidence from this admittedly small list of candidates that tools based on evolutionary conservation are effective at identifying risk variants reliably.
In general, approximately two-thirds of randomly occurring point mutations in coding sequence would alter an amino acid, and the fact that non-synonymous coding SNPs comprise less than one half of coding SNPs in the genome implies a strong selection against amino acid altering changes (Cargill et al., 1999). A major interest in human genetics is to distinguish mutations that are functionally neutral from those that contribute to disease. Amino acid substitutions currently account for approximately half of the known gene lesions responsible for human inherited disease. It has been suggested that most rare missense variants are probably at least mildly deleterious and the accumulation of such low-risk variants may be the basis for complex diseases such as breast cancer (Kryukov et al., 2007; Stratton and Rahman, 2008). In the WECARE Study, we could only define a small fraction of all identified BRCA1 and BRCA2 missense variants as likely to have had a deleterious effect on breast cancer risk. The absence of an aggregate association between the remaining missense VUS and risk may indicate that there are very few additional clearly deleterious missense variants. However, this does not exclude the possibility that a few additional BRCA missense variants are functionally perturbed and associated with an increased breast cancer risk. For example, in this study we made no attempt to investigate the potential effect of sequence variants with respect to altering, adding or disrupting motifs of exonic splicing enhancers or silencers, or splice donor, acceptor or branch point sites. This analysis would include also synonymous and noncoding variants and add additional levels of complexity in interpreting the significance of BRCA sequence variants found in women with breast cancer.
In conclusion, this WECARE Study comprises a comprehensive effort in genetic screening of a large and uniform sample set, and resulted in a careful characterization of the landscape of BRCA1 and BRCA2 sequence variants in young women with breast cancer. One striking observation was the high frequency of rare missense variants that could not be unequivocally classified. We identified a number of new potentially deleterious missense mutations for further analysis and emphasize the large BRCA2 DNA binding domain as a possible target for additional candidates. Our overall conclusion, however, is that the majority of VUSs found in BRCA screening of affected women represent neutral alleles of no or little significance in the etiology of breast cancer.
WECARE STUDY COLLABORATIVE GROUP
Memorial Sloan Kettering Cancer Center (New York, NY): Jonine L. Bernstein Ph.D. (Study P.I.), Colin B. Begg. Ph.D., Marinela Capanu Ph.D., Xiaolin Liang M.D., Anne S. Reiner M.P.H., Tracy M. Layne M.P.H.; City of Hope (Duarte, CA): Leslie Bernstein Ph.D., Laura Donnelly-Allen; Danish Cancer Society (Copenhagen, Denmark): Jørgen H. Olsen M.D., D.M.Sc., Michael Andersson M.D., D.M.Sc., Lisbeth Bertelsen M.D.Ph.D., Per Guldberg Ph.D., Lene Mellemkjær Ph.D.;
Fred Hutchinson Cancer Research Center (Seattle, WA): Kathleen E. Malone Ph.D., Noemi Epstein; International Epidemiology Institute (Rockville, MD) and Vanderbilt University (Nashville, TN): John D. Boice
BRCA1 and BRCA2 Sequence Variants in Unilateral and Bilateral Breast Cancer E 1213
Jr. Sc.D.; Lund University (Lund, Sweden): Åke Borg Ph.D., Therese Törngren M.Sc., Lina Tellhed, B.Sc.; National Cancer Institute (Bethesda, MD): Daniela Seminara Ph.D. M.P.H.; New York University (New York, NY): Roy E. Shore Ph.D., Dr.PH.; Norwegian Radium Hospital (Oslo, Norway): Anne-Lise Børresen-Dale Ph.D., Laila Jansen; University of California at Irvine (Irvine, CA): Hoda Anton-Culver, Ph.D., Joan Largent Ph.D. M.P.H.; University of Iowa (Iowa City, IA): Charles F. Lynch M.D., Ph.D., Jeanne DeWall M.A.; University of Southern California (Los Angeles, CA): Robert W. Haile DrPH., Bryan M. Langholz Ph.D., Duncan C. Thomas Ph.D., Shanyan Xue M.D., Nianmin Zhou, M.D, Anh T. Diep, Evgenia Ter-Karapetova; University of Southern Maine (Portland, ME):W. Douglas Thompson Ph.D.; University of Texas, M.D. Anderson Cancer Center (Houston, TX): Marilyn Stovall Ph.D., Susan Smith M.P.H.; University of Virginia (Charlottesville, VA): Patrick Concannon, Ph.D., Sharon Teraoka, Ph.D., Eric R. Olson, Nirasha Ramchurren, Ph.D.
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E 12
16 B
org
et al
.
Supp
. Tab
le S1
. Dele
terio
us B
RCA1
and
BRCA
2 mut
aton
s ide
ntifi
ed in
705 c
ontra
later
al (C
BC) a
nd 13
98 u
nilat
eral
brea
st ca
ncer
pat
ients
(UBC
).
Gen
eE
xon
NT
1B
ase
Cha
nge
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A1
2 18
5 de
l AG
St
op 3
9 18
5del
AG
c.
68_6
9del
AG
p.
Glu
23fs
F
16
12
4 B
RC
A1
2 18
8 in
s AG
St
op 3
1 18
8ins
AG
c.
68_6
9dup
AG
p.
Cys
24fs
F
2 2
B
RC
A1
3 20
2 de
l TG
St
op 3
9 20
2del
TG
c.83
_84d
elTG
p.
Leu2
8fs
F 1
1
BR
CA
1 3
249
T to
A
Cys
to S
er
C44
S c.
130T
>A
p.C
ys44
Ser
M
2 2
B
RC
A1
5 29
7 de
l CA
St
op 6
4 29
7del
CA
c.
178_
179d
elC
A
p.G
ln60
fs
F 1
1
BR
CA
1 5
300
T to
G
Cys
to G
ly
C61
G
c.18
1T>G
p.
Cys
61G
ly
M
10
8 2
BR
CA
1 5
330
A to
G
Arg
to G
ly
R71
G
c.21
1A>G
p.
Arg
71G
ly
S 1
1
BR
CA
1 7
421-
2 de
l A
- IV
S6-2
delA
c.
302-
2del
A
S
1 1
B
RC
A1
7 54
6 G
to T
G
lu to
Sto
p E1
43X
c.
427G
>T
p.G
lu14
3X
N
1
1 B
RC
A1
8 60
4 de
l TG
St
op 1
80
604d
elTG
c.
485_
486d
elTG
p.
Val
162f
s F
1 1
B
RC
A1
10
713-
2 A
to C
-
IVS9
-2A
>C
c.59
4-2A
>C
S
1 1
B
RC
A1
11
1201
de
l 11
Stop
361
12
01de
l11
c.10
82_1
092d
el11
p.
Ser3
61X
F
1
1 B
RC
A1
11
1240
de
l C
Stop
375
12
40de
lC
c.11
21de
lC
p.Th
r374
fs
F 1
1
BR
CA
1 11
16
23
del T
TAA
A
Stop
503
16
23de
l5
c.15
04_1
508d
el5
p.Le
u502
fs
F 2
1 1
BR
CA
1 11
16
48
C to
A
Ser t
o St
op
S510
X
c.15
29C
>A
p.Se
r510
X
N
1
1 B
RC
A1
11
1675
de
l A
Stop
531
16
75de
lA
c.15
56de
lA
p.Ly
s519
fs
F 2
2
BR
CA
1 11
18
06
C to
T
Gln
to S
top
Q56
3X
c.16
87C
>T
p.G
ln56
3X
N
1 1
B
RC
A1
11
1921
de
l 248
St
op 6
03
1921
del2
48
c.18
02_2
049d
el24
8 p.
His
601f
s F
1 1
B
RC
A1
11
2154
A
to T
Ly
s to
Stop
K
679X
c.
2035
A>T
p.
Lys6
79X
N
1
1
BR
CA
1 11
24
33
del G
St
op 7
91
2433
delG
c.
2314
delG
p.
Val
772f
s F
1
1 B
RC
A1
11
2508
de
l G
Stop
802
25
08de
lG
c.23
89de
lG
p.G
lu79
7fs
F 1
1
BR
CA
1 11
25
52
del C
St
op 8
14
2552
delC
c.
2433
delC
p.
Lys8
12fs
F
1
1 B
RC
A1
11
2594
de
l C
Stop
845
25
94de
lC
c.24
75de
lC
p.A
sp82
5fs
F 3
1 2
BR
CA
1 11
26
34
del C
St
op 8
45
2634
delC
c.
2515
delC
p.
His
839f
s F
1 1
B
RC
A1
11
2754
G
to T
G
lu to
Sto
p E8
79X
c.
2635
G>T
p.
Glu
879X
N
1
1
BR
CA
1 11
27
98
del G
AA
A
Stop
998
27
98de
l4
c.26
79_2
682d
elG
AA
A
p.Ly
s893
fs
F 1
1
BR
CA
1 11
28
41
G to
T
Glu
to S
top
E908
X
c.27
22G
>T
p.G
lu90
8X
N
1 1
B
RC
A1
11
2983
C
to A
Se
r to
Stop
S9
55X
c.
2864
C>A
p.
Ser9
55X
N
1
1
BR
CA
1 11
31
24
del A
St
op 1
023
3124
delA
c.
3005
delA
p.
Asn
1002
fs
F 1
1
BR
CA
1 11
31
48
del C
T St
op 1
016
3148
delC
T c.
3029
_303
0del
CT
p.Pr
o101
0fs
F 1
1
BR
CA
1 11
31
71
ins T
GA
GA
St
op 1
025
3171
ins5
c.
3048
_305
2dup
5 p.
Asn
1018
fs
F 1
1
BR
CA
1 11
33
07
del C
C in
s G
Stop
106
3 33
07de
lCC
insG
c.
3188
_318
9del
CC
insG
p.
Ser1
063X
F
1
1 B
RC
A1
11
3347
de
l AG
St
op 1
084
3347
delA
G
c.32
28_3
229d
elA
G
p.G
ly10
77fs
F
1 1
B
RC
A1
11
3438
G
to T
G
lu to
Sto
p E1
107X
c.
3319
G>T
p.
Glu
1107
fs
N
2 2
B
RC
A1
11
3450
de
l CA
AG
St
op 1
115
3450
del4
c.
3331
_333
4del
CA
AG
p.
Gln
1111
fs
F 1
1
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
17
Gen
eE
xon
NT
1B
ase
Cha
nge
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A1
11
3508
C
to G
Se
r to
Stop
S1
130X
c.
3389
C>G
p.
Ser1
130X
N
1
1
BR
CA
1 11
36
00
del 1
1 St
op 1
163
3600
del1
1 c.
3481
_349
1del
11
p.G
lu11
61fs
F
2 2
B
RC
A1
11
3726
C
to T
A
rg to
Sto
p R
1203
X
c.36
07C
>T
p.A
rg12
03X
N
3
1 2
BR
CA
1 11
38
29
del T
St
op 1
263
3829
delT
c.
3710
delT
p.
Ile12
37fs
F
1 1
B
RC
A1
11
3867
G
to T
G
lu to
Sto
p E1
250X
c.
3748
G>T
p.
Glu
1250
X
N
4 2
2 B
RC
A1
11
3875
de
l GTC
T St
op 1
262
3875
del4
c.
3756
_375
9del
GTC
T p.
Ser1
253f
s F
4 4
B
RC
A1
11
4184
de
l TC
AA
St
op 1
364
4184
del4
c.
4065
_406
8del
TCA
A
p.A
sn13
55fs
F
2
2 B
RC
A1
12
4302
C
to T
G
ln to
Sto
p Q
1395
X
c.41
83C
>T
p.G
ln13
95X
N
1
1
BR
CA
1 13
43
41
C to
T
Gln
to S
top
Q14
08X
c.
4222
C>T
p.
Gln
1408
X
N
1
1 B
RC
A1
13
4370
de
l GT
Stop
142
6 43
70de
lGT
c.42
51_4
252d
elG
T p.
Leu1
418f
s F
1 1
B
RC
A1
13
4446
C
to T
A
rg to
Sto
p R
1443
X
c.43
27C
>T
p.A
rg14
43X
N
2
1 1
BR
CA
1 13
44
76+1
G
to T
-
IVS1
3+1G
>T
c.43
57+1
G>T
S 2
1 1
BR
CA
1 16
51
05+2
T
to C
-
IVS1
6+2T
>C
c.49
86+2
T>C
S 1
1
BR
CA
1 18
52
14
C>T
A
rg to
Trp
R
1699
W
c.50
95C
>T
p.A
rg16
99Tr
p M
1
1
BR
CA
1 18
52
42
C>A
A
la to
Glu
A
1708
E c.
5123
C>A
p.
Ala
1708
Glu
M
1
1
BR
CA
1 20
53
32
G to
A
Gly
to G
lu
G17
38E
c.52
13G
>A
p.G
ly17
38G
lu
M
1
1
BR
CA
1 20
53
49
del A
St
op 1
764
5349
delA
c.
5230
delA
p.
Arg
1744
fs
F 1
1
BR
CA
1 20
53
82
ins C
St
op 1
829
5382
insC
c.
5266
dupC
p.
Gln
1756
fs
F 10
2
8 B
RC
A1
21
5443
T
to G
M
et to
Arg
M
1775
R
c.53
24T>
G
p.M
et17
75A
rg
M
1
1 B
RC
A1
23
5563
G
to A
Tr
p to
Sto
p W
1815
X
c.54
44G
>A
p.Tr
p181
5X
N
1
1 B
RC
A1
24
5622
C
to T
A
rg to
Sto
p R
1835
X
c.55
03C
>T
p.A
rg18
35X
N
1
1
BR
CA
1 24
56
77
ins A
St
op 1
853
5677
insA
c.
5558
dupA
p.
Tyr1
853X
F
1 1
B
RC
A1
Tota
l
10
9 67
42
B
RC
A2
2 23
1 G
to A
M
et to
Ile
M1I
c.
3G>A
p.
Met
1Ile
M
1
1
BR
CA
2 2
279
del A
C
Stop
29
279d
elA
C
c.51
_52d
elA
C
p.A
rg18
fs
F 1
1
BR
CA
2 4
592
del A
St
op 1
35
592d
elA
c.
364d
elA
p.
Thr1
22fs
F
1 1
B
RC
A2
5 69
7 de
l AA
St
op 1
81
697d
elA
A
c.46
9_47
0del
AA
p.
Lys1
57fs
F
1
1 B
RC
A2
7 83
8 de
l C
Stop
210
83
8del
C
c.61
0del
C
p.Le
u204
fs
F 1
1
BR
CA
2 9
983
del A
CA
G
Stop
275
98
3del
4 c.
755_
758d
elA
CA
G
p.A
sp25
2fs
F 2
1 1
BR
CA
2 10
14
61
ins A
St
op 4
20
1461
insA
c.
1233
dupA
p.
Pro4
12fs
F
1
1 B
RC
A2
10
1538
de
l AA
GA
St
op 4
58
1538
del4
c.
1310
_131
3del
AA
GA
p.
Lys4
37fs
F
3 3
B
RC
A2
10
1898
de
l 14
Stop
557
18
98de
l14
c.16
70_1
683d
el14
p.
Leu5
57X
F
1 1
B
RC
A2
10
2034
de
l A
Stop
613
20
34de
lA
c.18
13de
lA
p.Ile
605f
s F
1 1
B
RC
A2
10
2041
in
s A
Stop
615
20
41in
sA
c.18
13du
pA
p.Ile
605f
s F
3 2
1 B
RC
A2
11
2482
de
l GA
CT
Stop
770
24
82de
l4
c.22
54_2
257d
elG
AC
T p.
Asp
752f
s F
1 1
B
RC
A2
11
2600
C
to A
Se
r to
Stop
S7
91X
c.
2372
C>A
p.
Ser7
91X
N
1
1
E 12
18 B
org
et al
.
Gen
eE
xon
NT
1B
ase
Cha
nge
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
11
3036
de
l AC
AA
St
op 9
58
3036
del4
c.
2808
_281
1del
AC
AA
p.
Ala
938f
s F
5 4
1 B
RC
A2
11
3058
A
to T
Ly
s to
Stop
K
944X
c.
2830
A>T
p.
Lys9
44X
N
1
1
BR
CA
2 11
33
37
C to
T
Gln
to S
top
Q10
37X
c.
3109
C>T
p.
Gln
1037
X
N
1 1
B
RC
A2
11
3492
in
s T
Stop
109
8 34
92in
sT
c.32
64du
pT
p.G
ln10
89fs
F
1
1 B
RC
A2
11
3773
de
l TT
Stop
118
2 37
73de
lTT
c.35
45_3
546d
elTT
p.
Phe1
182X
F
1
1 B
RC
A2
11
3827
de
l GT
Stop
120
0 38
27de
lGT
c.35
99_3
600d
elG
T p.
Cys
1200
X
F 1
1
BR
CA
2 11
40
75
del G
T St
op 1
284
4075
delG
T c.
3847
_384
8del
GT
p.V
al12
83fs
F
1 1
B
RC
A2
11
4093
de
l AA
AT
Stop
129
1 40
93de
l4
c.38
65_3
868d
elA
AA
T p.
Lys1
289f
s F
1
1 B
RC
A2
11
4206
in
s TG
CT
Stop
133
0 42
06in
s4
c.39
75_3
978d
upTT
GC
p.
Ala
1327
fs
F 1
1
BR
CA
2 11
46
77
del A
St
op 1
485
4677
delA
c.
4449
delA
p.
Asp
1484
fs
F 1
1
BR
CA
2 11
51
64
del G
AA
A
Stop
166
8 51
64de
l4
c.49
36_4
939d
elG
AA
A
p.G
lu16
46fs
F
1 1
B
RC
A2
11
5804
de
l TTA
A
Stop
186
1 58
04de
l4
c.55
76_5
579d
elTT
AA
p.
Ile18
59fs
F
1
1 B
RC
A2
11
5844
de
l AG
TAA
St
op 1
873
5844
del5
c.
5616
_562
0del
5 p.
Lys1
872f
s F
1
1 B
RC
A2
11
5873
C
to A
Se
r to
Stop
S1
882X
c.
5645
C>A
p.
Ser1
882X
N
1
1
BR
CA
2 11
59
10
C to
G
Tyr t
o St
op
Y18
94X
c.
5682
C>G
p.
Tyr1
894X
N
1
1
BR
CA
2 11
59
50
del C
T St
op 1
909
5950
delC
T c.
5722
_572
3del
CT
p.Le
u190
8fs
F 2
1 1
BR
CA
2 11
61
74
del T
St
op 2
003
6174
delT
c.
5946
delT
p.
Ser1
982f
s F
5 2
3 B
RC
A2
11
6286
G
to T
G
lu to
Sto
p E2
020X
c.
6058
G>T
p.
Glu
2020
X
N
1
1 B
RC
A2
11
6503
de
l TT
Stop
209
8 65
03de
lTT
c.62
75_6
276d
elTT
p.
Leu2
092f
s F
1
1 B
RC
A2
11
6633
de
l CTT
AA
St
op 2
137
6633
del5
c.
6405
_640
9del
5 p.
Asn
2135
fs
F 1
1
BR
CA
2 11
66
71
del C
T St
op 2
149
6671
delC
T c.
6443
_644
4del
CT
p.Se
r214
8fs
F 1
1
BR
CA
2 11
67
14
del A
CA
A
Stop
216
6 67
14de
l4
c.64
86_6
489d
elA
CA
A
p.Ly
s216
2fs
F 1
1
BR
CA
2 11
68
84
C to
G
Ser t
o St
op
S221
9X
c.66
56C
>G
p.Se
r221
9X
N
1
1 B
RC
A2
13
7169
de
l C
Stop
231
5 71
69de
lC
c.69
41de
lC
p.Th
r231
4fs
F 1
1
BR
CA
2 14
72
53
del A
A
Stop
235
8 72
53de
lAA
c.
7025
_702
6del
AA
p.
Gln
2342
fs
F 1
1
BR
CA
2 14
72
95
del T
T St
op 2
358
7295
delT
T c.
7067
_706
8del
TT
p.Ph
e235
6fs
F 1
1
BR
CA
2 14
72
97
del C
T St
op 2
358
7297
delC
T c.
7069
_707
0del
CT
p.Le
u235
7fs
F 2
1 1
BR
CA
2 14
74
38
del 7
insT
G
Stop
241
0 74
38de
l7in
s2
c.72
10_7
216d
el7i
nsTG
p.
Lys2
404f
s F
1
1 B
RC
A2
15
7786
C
to T
A
rg to
Sto
p R
2520
X
c.75
58C
>T
p.A
rg25
20X
N
1
1
BR
CA
2 16
79
90
del A
TA in
s TT
Stop
264
7 79
90de
l3in
s2
c.77
62_7
764d
elA
TAin
sTT
p.Ile
2588
fs
F 1
1
BR
CA
2 17
81
41
del T
TCC
T St
op 2
638
8141
del5
c.
7913
_791
7del
5 p.
Phe2
638X
F
1 1
B
RC
A2
18
8550
in
s T
Stop
278
1 85
50in
sT
c.83
22du
pT
p.M
et27
75fs
F
1 1
B
RC
A2
18
8558
de
l A
Stop
282
0 85
58de
lA
c.83
30de
lA
p.Ly
s277
7fs
F 1
1
BR
CA
2 20
88
03
del C
St
op 2
862
8803
delC
c.
8575
delC
p.
Gln
2859
fs
F 1
1
BR
CA
2 20
88
23
ins T
St
op 2
868
8823
insT
c.
8594
dupT
p.
Leu2
865f
s F
1 1
B
RC
A2
21
8958
de
l T
Stop
292
6 89
58de
lT
c.87
30de
lT
p.A
sn29
10fs
F
1 1
B
RC
A2
22
9181
+1
G to
T
- IV
S22+
1G>T
c.
8953
+1G
>T
S
1 1
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
19
Gen
eE
xon
NT
1B
ase
Cha
nge
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
23
9197
G
to A
Tr
p to
Sto
p W
2990
X
c.89
69G
>A
p.Tr
p299
0fs
N
1
1 B
RC
A2
23
9326
in
s A
Stop
304
3 93
26in
sA
c.90
97du
pA
p.Th
r303
3fs
F 1
1
BR
CA
2 24
94
81
ins A
St
op 3
110
9481
insA
c.
9253
dupA
p.
Thr3
085f
s F
1 1
B
RC
A2
25
9610
C
to T
A
rg to
Sto
p R
3128
X
c.93
82C
>T
p.A
rg31
28X
N
1
1
BR
CA
2 25
97
29+3
A
to T
-
IVS2
5+3A
>T
c.95
01+3
A>T
S 2
2
BR
CA
2 26
97
69
del 1
4 St
op 3
183
9769
del1
4 c.
9541
_955
4del
14
p.M
et31
81fs
F
1 1
B
RC
A2
Tota
l
72
41
31
1 BR
CA
1: n
ucle
otid
e nu
mbe
r acc
ordi
ng to
Gen
Ban
k U
1468
0.1.
http
://w
ww
.ncb
i.nlm
.nih
.gov
/ent
rez/
view
er.fc
gi?d
b=nu
cleo
tide&
val=
5559
31
1 BR
CA
2: n
ucle
otid
e nu
mbe
r acc
ordi
ng to
Gen
Bank
NM
_000
059.
1. h
ttp://
ww
w.n
cbi.n
lm.n
ih.g
ov/e
ntre
z/vi
ewer
.fcgi
?db=
nucl
eotid
e&va
l=45
0245
0 2 B
IC (B
reas
t Can
cer I
nfor
mat
ion
Cor
e). h
ttp://
rese
arch
.nhg
ri.ni
h.go
v/bi
c/
3 HG
VS
(Hum
an G
enom
e V
aria
tion
Soci
ety)
. http
://w
ww
.hgv
s.org
/mut
nom
en/re
cs.h
tml
4 Typ
e: F
=fra
me
shift
, M=m
isse
nse,
S=s
plic
e si
te, N
=non
sens
e 5 N
umbe
r of o
bser
vatio
ns
mut
atio
ns n
ot e
arlie
r des
crib
ed in
BIC
(by
Nov
embe
r 200
8)
E 12
20 B
org
et al
.
Supp
. Tab
le S2
. BRC
A1 an
d BR
CA2 u
nclas
sified
varia
nts i
dent
ified
in 70
5 con
tralat
eral
(CBC
) and
1398
uni
later
al br
east
canc
er p
atien
ts (U
BC).
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A1
2 10
1-10
T
to C
-
IV
S1-1
0T>C
c.
-29T
>C
IV
S 1
10
BR
CA
1 3
200-
129
G to
A
- IV
S2-1
29G
>A
c.81
-129
G>A
IVS
10
1 B
RC
A1
3 20
0-55
T
to G
-
IVS2
-55T
>G
c.81
-55T
>G
IV
S 1
01
BR
CA
1 3
233
G to
A
Lys t
o Ly
s K
38K
c.
114T
>A
p.=
Syn
33
0 B
RC
A1
3 25
3 A
to C
Ly
s to
Thr
K45
T c.
134A
>C
p.Ly
s45T
hr
M
10
1 B
RC
A1
5 25
4-53
T
to C
-
IVS4
-53T
>C
c.13
5-53
T>C
IVS
10
1 B
RC
A1
5 25
4-23
C
to T
-
IVS4
-23C
>T
c.13
5-23
C>T
IVS
10
1 B
RC
A1
5 33
1+23
T
to A
-
IVS5
+23T
>A
c.21
2+23
T>A
IVS
41
3 B
RC
A1
7 42
1-70
G
to A
-
IVS6
-70G
>A
c.30
2-70
G>A
IVS
10
1 B
RC
A1
7 43
3 A
to G
Ty
r to
Cys
Y
105C
c.
314A
>G
p.Ty
r105
Cys
M
1
01
BR
CA
1 7
544
C to
A
Pro
to H
is
P142
H
c.42
5C>A
p.
Pro1
42H
is
M
42
2 B
RC
A1
7 56
0+36
de
l 14
- IV
S7+3
6del
14
c.44
1+36
del1
4
IVS
1154
377
777
BR
CA
1 8
561-
34
C to
T
- IV
S7-3
4C>T
c.
442-
34C
>T
IV
S 77
925
452
5 B
RC
A1
8 62
8 G
to A
A
rg to
Gln
R
170Q
c.
509G
>A
p.A
rg17
0Gln
M
2
11
BR
CA
1 8
655
A to
G
Tyr t
o C
ys
Y17
9C
c.53
6A>G
p.
Tyr1
79C
ys
M
20
2 B
RC
A1
9 66
7-80
T>
C
- IV
S8-8
0T>C
c.
548-
80T>
C
IV
S 5
32
BR
CA
1 9
667-
58
delT
-
IVS8
-58d
elT
c.54
8-58
delT
IVS
1044
342
702
BR
CA
1 9
667-
17
G to
T
- IV
S8-1
7G>T
c.
548-
17G
>T
IV
S 2
11
BR
CA
1 9
667-
3 de
l T
- IV
S8-3
delT
c.
548-
3del
T
IVS
10
1 B
RC
A1
9 71
0 C
to T
C
ys to
Cys
C
197C
c.
591C
>T
p.=
Syn
31
2 B
RC
A1
10
713-
72
A>G
-
IVS9
-72A
>G
c.59
4-72
A>G
IVS
11
0 B
RC
A1
10
713-
34
T to
C
- IV
S9-3
4T>C
c.
594-
34T>
C
IV
S 1
01
BR
CA
1 10
76
0 A
to G
A
sp to
Gly
D
214G
c.
641A
>G
p.A
sp21
4Gly
M
1
10
BR
CA
1 11
81
2 G
to A
Th
r to
Thr
T231
T c.
693G
>A
p.=
Syn
10
1 B
RC
A1
11
855
T to
G
Leu
to V
al
L246
V
c.73
6T>G
p.
Leu2
46V
al
M
32
1 B
RC
A1
11
944
C to
T
Gly
to G
ly
G27
5G
c.82
5C>T
p.
= Sy
n 1
01
BR
CA
1 11
10
67
C to
G
Ser t
o A
rg
S316
R
c.94
8C>G
p.
Ser3
16A
rg
M
10
1 B
RC
A1
11
1100
A
to G
Th
r to
Thr
T327
T c.
981A
>G
p.=
Syn
40
4 B
RC
A1
11
1152
G
to T
A
sp to
Tyr
D
345Y
c.
1033
G>T
p.
Asp
345T
yr
M
11
0 B
RC
A1
11
1184
G
to A
Ly
s to
Lys
K35
5K
c.10
65G
>A
p.=
Syn
10
1 B
RC
A1
11
1186
A
to G
G
ln to
Arg
Q
356R
c.
1067
A>G
p.
Gln
356A
rg
M
251
8117
0 B
RC
A1
11
1224
de
l GA
T de
l Asp
D
369d
el
c.11
05de
lGA
T p.
Asp
369d
el
IFD
1
01
BR
CA
1 11
12
56
T to
G
Ile to
Met
I3
79M
c.
1137
T>G
p.
Ile37
9Met
M
1
01
BR
CA
1 11
15
75
T to
C
Phe
to L
eu
F486
L c.
1456
T>C
p.
Phe4
86Le
u M
4
13
BR
CA
1 11
16
05
C to
T
Arg
to C
ys
R49
6C
c.14
86C
>T
p.A
rg49
6Cys
M
2
11
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
21
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A1
11
1606
G
to A
A
rg to
His
R
496H
c.
1487
G>A
p.
Arg
496H
is
M
40
4 B
RC
A1
11
1728
A
to G
A
sn to
Asp
N
537D
c.
1609
A>G
p.
Asn
537A
sp
M
10
1 B
RC
A1
11
1767
A
to C
A
sn to
His
N
550H
c.
1648
A>C
p.
Asn
550H
is
M
31
2 B
RC
A1
11
1831
T
to C
Ile
to T
hr
I571
T c.
1712
T>C
p.
Ile57
1Thr
M
1
01
BR
CA
1 11
19
08
G to
A
Glu
to L
ys
E597
K
c.17
89G
>A
p.G
lu59
7Lys
M
3
03
BR
CA
1 11
19
65
del T
CT
del S
er
S616
del
c.18
46de
lTC
T p.
Ser6
16de
l IF
D
10
1 B
RC
A1
11
1984
C
to T
A
la to
Val
A
622V
c.
1865
C>T
p.
Ala
622V
al
M
11
0 B
RC
A1
11
2030
T
to C
Th
r to
Thr
T637
T c.
1911
T>C
p.
= Sy
n 1
01
BR
CA
1 11
20
90
A to
G
Gln
to G
ln
Q65
7Q
c.19
71A
>G
p.=
Syn
30
3 B
RC
A1
11
2196
G
to A
A
sp to
Asn
D
693N
c.
2077
G>A
p.
Asp
693A
sn
M
296
106
190
BR
CA
1 11
22
01
C to
T
Ser t
o Se
r S6
94S
c.20
82C
>T
p.=
Syn
1040
337
703
BR
CA
1 11
24
18
A to
G
Ser t
o G
ly
S767
G
c.22
99A
>G
p.Se
r767
Gly
M
1
01
BR
CA
1 11
24
30
T to
C
Leu
to L
eu
L771
L c.
2311
T>C
p.
= Sy
n 98
732
166
6 B
RC
A1
11
2471
G
to A
Se
r to
Ser
S784
S c.
2352
G>A
p.
= Sy
n 1
10
BR
CA
1 11
25
35
G to
A
Ala
to T
hr
A80
6T
c.24
16G
>A
p.A
la80
6Thr
M
1
10
BR
CA
1 11
25
77
A to
G
Lys t
o G
lu
K82
0E
c.24
58A
>G
p.Ly
s820
Glu
M
5
14
BR
CA
1 11
25
92
G to
T
Asp
to T
yr
D82
5Y
c.24
73G
>T
p.A
sp82
5Tyr
M
1
10
BR
CA
1 11
25
96
C to
A
Thr t
o Ly
s T8
26K
c.
2477
C>A
p.
Thr8
26Ly
s M
1
01
BR
CA
1 11
26
02
del G
CT
del G
ly 8
28
G82
8del
c.
2483
delG
CT
p.G
ly82
8del
IF
D
10
1 B
RC
A1
11
2637
A
to G
Se
r to
Gly
S8
40G
c.
2518
A>G
p.
Ser8
40G
ly
M
10
1 B
RC
A1
11
2640
C
to T
A
rg to
Trp
R
841W
c.
2521
C>T
p.
Arg
841T
rp
M
82
6 B
RC
A1
11
2641
G
to A
A
rg to
Gln
R
841Q
c.
2522
G>A
p.
Arg
841G
ln
M
10
1 B
RC
A1
11
2685
T
to C
Ty
r to
His
Y
856H
c.
2566
T>C
p.
Tyr8
56H
is
M
11
0 B
RC
A1
11
2715
C
to T
A
rg to
Cys
R
866C
c.
2596
C>T
p.
Arg
866C
ys
M
10
1 B
RC
A1
11
2727
G
to C
A
la to
Pro
A
870P
c.
2608
G>C
p.
Ala
870P
ro
M
11
0 B
RC
A1
11
2731
C
to T
Pr
o to
Leu
P8
71L
c.26
12C
>T
p.Pr
o871
Leu
M
1029
333
696
BR
CA
1 11
28
47
C to
G
Gln
to G
lu
Q91
0E
c.27
28C
>G
p.G
ln91
0Glu
M
1
01
BR
CA
1 11
28
52
A to
G
Gly
to G
ly
G91
1G
c.27
33A
>G
p.=
Syn
50
5 B
RC
A1
11
2933
A
to G
Pr
o to
Pro
P9
38P
c.28
14A
>G
p.=
Syn
20
2 B
RC
A1
11
3003
G
to A
G
lu to
Lys
E9
62K
c.
2884
G>A
p.
Glu
962L
ys
M
10
1 B
RC
A1
11
3119
G
to A
G
lu to
Glu
E1
000E
c.
3000
G>A
p.
= Sy
n 1
10
BR
CA
1 11
31
43
G to
A
Met
to Il
e M
1008
I c.
3024
G>A
p.
Met
1008
Ile
M
40
4 B
RC
A1
11
3232
A
to G
G
lu to
Gly
E1
038G
c.
3113
A>G
p.
Glu
1038
Gly
M
99
632
467
2 B
RC
A1
11
3238
G
to A
Se
r to
Asn
S1
040N
c.
3119
G>A
p.
Ser1
040A
sn
M
7328
45
BR
CA
1 11
33
40
G to
C
Arg
to T
hr
R10
74T
c.32
21G
>C
p.A
rg10
74Th
r M
1
10
BR
CA
1 11
34
15
C to
T
Pro
to L
eu
P109
9L
c.32
96C
>T
p.Pr
o109
9Leu
M
1
01
BR
CA
1 11
34
21
G to
A
Ser t
o A
sn
S110
1N
c.33
02G
>A
p.Se
r110
1Asn
M
2
02
BR
CA
1 11
35
35
G to
T
Ser t
o Ile
S1
139I
c.
3416
G>T
p.
Ser1
139I
le
M
11
0
E 12
22 B
org
et al
.
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A1
11
3537
A
to G
Se
r to
Gly
S1
140G
c.
3418
A>G
p.
Ser1
140G
ly
M
20
2 B
RC
A1
11
3573
G
to A
A
sp to
Asn
D
1152
N
c.34
54G
>A
p.A
sp11
52A
sn
M
10
1 B
RC
A1
11
3667
A
to G
Ly
s to
Arg
K
1183
R
c.35
48A
>G
p.Ly
s118
3Arg
M
99
832
867
0 B
RC
A1
11
3719
G
to C
G
ln to
His
Q
1200
H
c.36
00G
>C
p.G
ln12
00H
is
M
22
0 B
RC
A1
11
3727
G
to A
A
rg to
Gln
R
1203
Q
c.36
08G
>A
p.A
rg12
03G
ln
M
10
1 B
RC
A1
11
3827
T
to G
A
sn to
Lys
N
1236
K
c.37
08T>
G
p.A
sn12
36Ly
s M
1
01
BR
CA
1 11
38
36
T to
A
Ser t
o Se
r S1
239S
c.
3717
T>A
p.
= Sy
n 1
10
BR
CA
1 11
38
64
A to
C
Thr t
o Pr
o T1
249P
c.
3745
A>C
p.
Thr1
249P
ro
M
10
1 B
RC
A1
11
3916
G
to C
Se
r to
Thr
S126
6T
c.37
97G
>C
p.Se
r126
6Thr
M
2
11
BR
CA
1 11
39
42
A to
G
Ile to
Val
I1
275V
c.
3823
A>G
p.
Ile12
75V
al
M
10
1 B
RC
A1
11
4158
A
to G
A
rg to
Gly
R
1347
G
c.40
39A
>G
p.A
rg13
47G
ly
M
165
11
BR
CA
1 11
41
66
G to
T
Thr t
o Th
r T1
349T
c.
4047
G>T
p.
= Sy
n 1
01
BR
CA
1 11
42
15+3
A
to G
-
IVS1
1+3A
>G
c.40
96+3
A>G
IVS
11
0 B
RC
A1
11
4215
+39
T to
C
- IV
S11+
39T>
C
c.40
96+3
9T>C
IVS
10
1 B
RC
A1
12
4216
-28
A to
G
- IV
S11-
28A
>G
c.40
97-2
8A>G
IVS
11
0 B
RC
A1
12
421
6-11
T
to C
-
IVS1
1-11
T>C
c.
4097
-11T
>C
IV
S 1
01
BR
CA
1 12
42
30
G to
C
Gly
to A
rg
G13
71R
c.
4111
G>C
p.
Gly
1371
Arg
M
1
10
BR
CA
1 12
42
91
T to
C
Ile to
Thr
I1
391T
c.
4172
T>C
p.
Ile13
91Th
r M
1
10
BR
CA
1 12
43
04+2
0 de
l 18
- IV
S12+
20de
l18
c.41
85+2
0del
18
IV
S 1
01
BR
CA
1 12
43
04+2
1 de
l TG
-
IVS1
2+21
delT
G
c.41
85+2
1del
TG
IV
S 1
10
BR
CA
1 12
43
04+3
7 de
l TG
-
IVS1
2+37
delT
G
c.41
85+3
7del
TG
IV
S 2
20
BR
CA
1 13
44
27
C to
T
Ser t
o Se
r S1
436S
c.
4308
C>T
p.
= Sy
n 10
0532
368
2 B
RC
A1
13
4476
+17
A to
G
- IV
S13+
17A
>G
c.43
57+1
7A>G
IVS
10
1 B
RC
A1
14
4477
-37
G to
A
- IV
S13-
37G
>A
c.43
58-3
7G>A
IVS
11
0 B
RC
A1
14
4477
-28
T to
C
- IV
S13-
28T>
C
c.43
58-2
8T>C
IVS
11
0 B
RC
A1
14
447
7-10
C
to T
-
IVS1
3-10
C>T
c.
4358
-10C
>T
IV
S 2
11
BR
CA
1 14
45
29
A to
T
Glu
to A
sp
E147
0D
c.44
10A
>T
p.G
lu14
70A
sp
M
10
1 B
RC
A1
14
4603
+14
A to
G
- IV
S14+
14A
>G
c.44
84+1
4A>G
IVS
20
2 B
RC
A1
14
4603
+61
G to
T
- IV
S14+
61G
>T
c.44
84+6
1G>T
IVS
10
1 B
RC
A1
15
4654
G
to T
Se
r to
Ile
S151
2I
c.45
35G
>T
p.Se
r151
2Ile
M
18
315
B
RC
A1
15
4755
G
to A
A
sp to
Asn
D
1546
N
c.46
36G
>A
p.A
sp15
46A
sn
M
20
2 B
RC
A1
16
4869
G
to T
A
la to
Ser
A
1584
S c.
4750
G>T
p.
Ala
1584
Ser
M
11
0 B
RC
A1
16
4890
G
to A
G
ly to
Ser
G
1591
S c.
4771
G>A
p.
Gly
1591
Ser
M
11
0 B
RC
A1
16
4931
A
to G
G
ln to
Gln
Q
1604
Q
c.48
12A
>G
p.=
Syn
72
5 B
RC
A1
16
4956
A
to G
Se
r to
Gly
S1
613G
c.
4837
A>G
p.
Ser1
613G
ly
M
1069
348
721
BR
CA
1 16
50
02
T to
C
Met
to T
hr
M16
28T
c.48
83T>
C
p.M
et16
28Th
r M
1
01
BR
CA
1 16
50
75
G to
A
Met
to Il
e M
1652
I c.
4956
G>A
p.
Met
1652
Ile
M
6118
43
BR
CA
1 17
51
06-2
0 A
to G
-
IVS1
6-20
A>G
c.
4987
-20A
>G
IV
S 1
01
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
23
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A1
17
5124
G
to T
A
la to
Ser
A
1669
S c.
5005
G>T
p.
Ala
1669
Ser
M
10
1 B
RC
A1
18
5194
-53
C to
T
- IV
S17-
53C
>T
c.50
75C
>T
IV
S 11
431
83
BR
CA
1 20
53
13-4
3 T
to C
-
IVS1
9-43
T>C
c.
5194
-43T
>C
IV
S 1
01
BR
CA
1 20
53
96+6
0 in
s 12
- IV
S20+
60in
s12
c.52
77+6
0ins
12
IV
S 11
29
BR
CA
1 20
53
96+7
8 G
to A
-
IVS2
0+78
G>A
c.
5277
+78G
>A
IV
S 8
44
BR
CA
1 20
53
96+1
02
A to
G
- IV
S20+
102A
>G
c.52
77+1
02A
>G
IV
S 1
01
BR
CA
1 21
54
51+7
8 C
to T
-
IVS2
1+78
C>T
c.
5332
+78C
>T
IV
S 2
11
BR
CA
1 21
54
51+8
1 T
to C
-
IVS2
1+81
T>C
c.
5332
+81T
>C
IV
S 1
10
BR
CA
1 22
55
20
G to
T
Gly
to C
ys
G18
01C
c.
5401
G>T
p.
Gly
1801
Cys
M
1
01
BR
CA
1 22
55
25+3
3 A
to T
-
IVS2
2+33
A>T
c.
5406
+33A
>T
IV
S 2
02
BR
CA
1 22
55
25+6
8 T
to C
-
IVS2
2+68
T>C
c.
5406
+68T
>C
IV
S 6
24
BR
CA
1 23
55
30
T to
A
Val
to A
sp
V18
04D
c.
5411
T>A
p.
Val
1804
Asp
M
1
01
BR
CA
1 24
.5
587-
10
C to
A
- IV
S23-
10C
>A
c.54
68-1
0C>A
IVS
10
1 B
RC
A1
24
.558
7-8
G to
T
- IV
S23-
8G>T
c.
5468
-8G
>T
IV
S 1
01
BR
CA
1 24
56
88
C to
G
Gln
to G
lu
Q18
57E
c.55
69C
>G
p.G
ln18
57G
lu
M
11
0 B
RC
A1
24
5747
C
to G
-
U
GA
+36C
>G
c.*3
6C>G
UTR
5
14
BR
CA
1 24
58
07
C to
T
- U
GA
+96C
>T
c.*9
6C>T
UTR
1
10
BR
CA
2 2
203
G to
A
- 20
3G>A
c.
-26G
>A
U
TR
797
269
528
BR
CA
2 2
218
C to
T
- 21
8C>T
c.
-11C
>T
U
TR
10
1 B
RC
A2
2 29
5+62
T
to G
-
IVS2
+62T
>G
c.67
+62T
>G
IV
S 13
67
BR
CA
2 3
296-
31
A to
G
- IV
S2-3
1A>G
c.
68-3
1A>G
IVS
10
1 B
RC
A2
3 29
6-7
T to
A
- IV
S2-7
T>A
c.
68-7
T>A
IVS
101
9 B
RC
A2
3 35
3 A
to G
Ty
r to
Cys
Y
42C
c.
125A
>G
p.Ty
r42C
ys
M
113
8 B
RC
A2
3 40
7 A
to G
A
sn to
Ser
N
60S
c.17
9A>G
p.
Asn
60Se
r M
1
10
BR
CA
2 3
451
G to
C
Ala
to P
ro
A75
P c.
223G
>C
p.A
la75
Pro
M
22
0 B
RC
A2
3 49
5 G
to A
Pr
o to
Pro
P8
9P
c.26
7G>A
p.
= Sy
n 1
10
BR
CA
2 4
545-
37
insT
ATG
-
IVS3
-37i
nsTA
TG
c.31
7-37
insT
ATG
IVS
11
0 B
RC
A2
4 65
3+33
A
to G
-
IVS4
+33A
>G
c.42
5+33
A>G
IVS
11
0 B
RC
A2
5 65
4-37
T
to A
-
IVS4
-37T
>A
c.42
6-37
T>A
IVS
10
1 B
RC
A2
5 66
1 de
l GTT
de
l Val
V
145d
el
c.43
3del
GTT
p.
Val
145d
el
IFD
1
10
BR
CA
2 5
683
C to
A
Thr t
o Ly
s T1
52K
c.
455C
>A
p.Th
r152
Lys
M
10
1 B
RC
A2
5 69
5 A
to G
A
sp to
Gly
D
156G
c.
467A
>G
p.A
sp15
6Gly
M
1
10
BR
CA
2 6
744+
21
A to
T
- IV
S6+2
1A>T
c.
516+
21A
>T
IV
S 4
13
BR
CA
2 6
744+
54
T to
C
- IV
S6+5
4T>C
c.
516+
54T>
C
IV
S 3
21
BR
CA
2 6
744+
58
G to
A
- IV
S6+5
8G>A
c.
516+
58G
>A
IV
S 1
01
BR
CA
2 7
745-
19
C to
T
- IV
S6-1
9C>T
c.
517-
19C
>T
IV
S 1
10
BR
CA
2 7
823
G to
A
Ala
to T
hr
A19
9T
c.59
5G>A
p.
Ala
199T
hr
M
21
1
E 12
24 B
org
et al
.
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
7 85
9+25
C
to T
-
IVS7
+25C
>T
c.63
1+25
C>T
IVS
42
2 B
RC
A2
8 86
0-69
T
to C
-
IVS7
-69T
>C
c.63
2-69
T>C
IVS
62
4 B
RC
A2
8 86
0-64
G
to A
-
IVS7
-64G
>A
c.63
2-64
G>A
IVS
10
1 B
RC
A2
8 86
0-27
C
to G
-
IVS7
-27C
>G
c.63
2-27
C>G
IVS
10
1 B
RC
A2
9 91
0-32
A
to G
-
IVS8
-32A
>G
c.68
2-32
A>G
IVS
21
1 B
RC
A2
9 91
0-12
de
l TA
-
IVS8
-12d
elTA
c.
682-
12de
lTA
IVS
11
0 B
RC
A2
9 99
7 A
to C
A
sn to
His
N
257H
c.
769A
>C
p.A
sn25
7His
M
1
10
BR
CA
2 10
10
93
A to
C
Asn
to H
is
N28
9H
c.86
5A>C
p.
Asn
289H
is
M
148
5197
B
RC
A2
10
1184
A
to G
A
sn to
Ser
N
319S
c.
956A
>G
p.A
sn31
9Ser
M
1
01
BR
CA
2 10
11
92
A to
C
Lys t
o G
ln
K32
2Q
c.96
4A>C
p.
Lys3
22G
ln
M
10
1 B
RC
A2
10
1206
C
to A
Se
r to
Arg
S3
26R
c.
978C
>A
p.Se
r326
Arg
M
5
14
BR
CA
2 10
12
61
A to
G
Lys t
o G
lu
K34
5E
c.10
33A
>G
p.Ly
s345
Glu
M
1
01
BR
CA
2 10
12
68
A to
G
Gln
to A
rg
Q34
7R
c.10
40A
>G
p.G
ln34
7Arg
M
1
10
BR
CA
2 10
13
42
A to
C
Asn
to H
is
N37
2H
c.11
14A
>C
p.A
sn37
2His
M
10
2236
066
2 B
RC
A2
10
1379
C
to T
Se
r to
Phe
S384
F c.
1151
C>T
p.
Ser3
84Ph
e M
5
23
BR
CA
2 10
13
95
G to
A
Pro
to P
ro
P389
P c.
1167
G>A
p.
= Sy
n 1
10
BR
CA
2 10
14
60
T to
C
Ile to
Thr
I4
11T
c.12
32T>
C
p.Ile
411T
hr
M
10
1 B
RC
A2
10
1503
A
to G
G
lu to
Glu
E4
25E
c.12
75A
>G
p.=
Syn
11
0 B
RC
A2
10
1590
A
to G
Ly
s to
Lys
K45
4K
c.13
62A
>G
p.=
Syn
30
3 B
RC
A2
10
1593
A
to G
Se
r to
Ser
S455
S c.
1365
A>G
p.
= Sy
n 14
651
95
BR
CA
2 10
16
13
A to
G
Glu
to G
ly
E462
G
c.13
85A
>G
p.G
lu46
2Gly
M
1
01
BR
CA
2 10
16
75
G to
C
Ala
to P
ro
A48
3P
c.14
47G
>C
p.A
la48
3Pro
M
1
01
BR
CA
2 10
16
88
C to
A
Ala
to G
lu
A48
7E
c.14
60C
>A
p.A
la48
7Glu
M
3
03
BR
CA
2 10
16
94
C to
G
Ser t
o C
ys
S489
C
c.14
66C
>G
p.Se
r489
Cys
M
3
03
BR
CA
2 10
17
00
C to
G
Thr t
o Se
r T4
91S
c.14
72C
>G
p.Th
r491
Ser
M
10
1 B
RC
A2
10
1742
T
to C
Ile
to T
hr
I505
T c.
1514
T>C
p.
Ile50
5Thr
M
2
02
BR
CA
2 10
20
14
G to
C
Asp
to H
is
D59
6H
c.17
86G
>C
p.A
sp59
6His
M
3
21
BR
CA
2 10
20
16
T to
C
Asp
to A
sp
D59
6D
c.17
88T>
C
p.=
Syn
43
1 B
RC
A2
10
2020
A
to G
Th
r to
Ala
T5
98A
c.
1792
A>G
p.
Thr5
98A
la
M
115
6 B
RC
A2
10
2032
G
to A
G
ly to
Arg
G
602R
c.
1804
G>A
p.
Gly
602A
rg
M
11
0 B
RC
A2
10
2046
G
to A
Pr
o to
Pro
P6
06P
c.18
18G
>A
p.=
Syn
10
1 B
RC
A2
10
2117
C
to T
Th
r to
Ile
T630
I c.
1889
C>T
p.
Thr6
30Ile
M
1
01
BR
CA
2 10
21
37+2
3 in
s T
-
IVS1
0+23
insT
c.
1909
+23i
nsT
IV
S 5
05
BR
CA
2 11
21
39
T to
C
Gly
to G
ly
G63
7G
c.19
11T>
C
p.=
Syn
21
1 B
RC
A2
11
2166
C
to T
Se
r to
Ser
S646
S c.
1938
C>T
p.
= Sy
n 6
15
BR
CA
2 11
21
92
C to
G
Pro
to A
rg
P655
R
c.19
64C
>G
p.Pr
o655
Arg
M
7
25
BR
CA
2 11
23
10
T to
C
Asn
to A
sn
N69
4N
c.20
82T>
C
p.=
Syn
11
0 B
RC
A2
11
2457
T
to C
H
is to
His
H
743H
c.
2229
T>C
p.
= Sy
n 14
449
95
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
25
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
11
2578
A
to G
M
et to
Val
M
784V
c.
2350
A>G
p.
Met
784V
al
M
20
2 B
RC
A2
11
2640
A
to G
G
lu to
Glu
E8
04E
c.24
12A
>G
p.=
Syn
11
0 B
RC
A2
11
2778
A
to G
G
ln to
Gln
Q
850Q
c.
2550
A>G
p.
= Sy
n 1
01
BR
CA
2 11
29
37
A to
G
Leu
to L
eu
L903
L c.
2709
A>G
p.
= Sy
n 1
01
BR
CA
2 11
30
31
G to
A
Asp
to A
sn
D93
5N
c.28
03G
>A
p.A
sp93
5Asn
M
1
10
BR
CA
2 11
30
69
G to
T
Leu
to P
he
L947
F c.
2841
G>T
p.
Leu9
47Ph
e M
1
10
BR
CA
2 11
31
11
G to
A
Gln
to G
ln
Q96
1Q
c.28
83G
>A
p.=
Syn
41
3 B
RC
A2
11
3147
G
to A
Se
r to
Ser
S973
S c.
2919
G>A
p.
= Sy
n 1
01
BR
CA
2 11
31
85
A to
G
Asn
to S
er
N98
6S
c.29
57A
>G
p.A
sn98
6Ser
M
1
10
BR
CA
2 11
31
91
A to
C
Asp
to A
la
D98
8A
c.29
63A
>C
p.A
sp98
8Ala
M
1
10
BR
CA
2 11
31
99
A to
G
Asn
to A
sp
N99
1D
c.29
71A
>G
p.A
sn99
1Asp
M
14
851
97
BR
CA
2 11
32
83
C to
G
Leu
to V
al
L101
9V
c.30
55C
>G
p.Le
u101
9Val
M
1
01
BR
CA
2 11
34
14
T to
C
Pro
to P
ro
P106
2P
c.31
86T>
C
p.=
Syn
10
1 B
RC
A2
11
3444
A
to G
Le
u to
Leu
L1
072L
c.
3216
A>G
p.
= Sy
n 1
01
BR
CA
2 11
34
92
T to
C
Pro
to P
ro
P108
8P
c.32
64T>
C
p.=
Syn
40
4 B
RC
A2
11
3624
A
to G
Ly
s to
Lys
K11
32K
c.
3396
A>G
p.
= Sy
n 92
631
860
8 B
RC
A2
11
3645
G
to A
Ly
s to
Lys
K11
39K
c.
3417
G>A
p.
= Sy
n 1
01
BR
CA
2 11
36
48
T to
C
Ser t
o Se
r S1
140S
c.
3420
T>C
p.
= Sy
n 2
02
BR
CA
2 11
37
44
G to
A
Ser t
o Se
r S1
172S
c.
3516
G>A
p.
= Sy
n 4
04
BR
CA
2 11
39
45
A to
G
Lys t
o Ly
s K
1239
K
c.37
17A
>G
p.=
Syn
11
0 B
RC
A2
11
4035
T
to C
V
al to
Val
V
1269
V
c.38
07T>
C
p.=
Syn
651
212
439
BR
CA
2 11
40
42
A to
G
Met
to V
al
M12
72V
c.
3814
A>G
p.
Met
1272
Val
M
1
01
BR
CA
2 11
40
62
T to
C
His
to H
is
H12
78H
c.
3834
T>C
p.
= Sy
n 1
01
BR
CA
2 11
40
76
T to
C
Val
to A
la
V12
83A
c.
3848
T>C
p.
Val
1283
Ala
M
1
10
BR
CA
2 11
40
97
G to
A
Cys
to T
yr
C12
90Y
c.
3869
G>A
p.
Cys
1290
Tyr
M
41
3 B
RC
A2
11
4144
G
to A
V
al to
Ile
V13
06I
c.39
16G
>A
p.V
al13
06Ile
M
1
10
BR
CA
2 11
42
89
C to
T
Thr t
o M
et
T135
4M
c.40
61C
>T
p.Th
r135
4Met
M
2
11
BR
CA
2 11
42
96
G to
A
Leu
to L
eu
L135
6L
c.40
68G
>A
p.=
Syn
156
9 B
RC
A2
11
4318
A
to C
Ile
to L
eu
I136
4L
c.40
90A
>C
p.Ile
1364
Leu
M
20
2 B
RC
A2
11
4415
A
to G
G
ln to
Arg
Q
1396
R
c.41
87A
>G
p.G
ln13
96A
rg
M
11
0 B
RC
A2
11
4452
G
to A
G
ln to
Gln
Q
1408
Q
c.42
24G
>A
p.=
Syn
11
0 B
RC
A2
11
4469
C
to T
Th
r to
Met
T1
414M
c.
4241
C>T
p.
Thr1
414M
et
M
10
1 B
RC
A2
11
4486
G
to T
A
sp to
Tyr
D
1420
Y
c.42
58G
>T
p.A
sp14
20Ty
r M
31
625
B
RC
A2
11
4587
A
to G
Ly
s to
Lys
K14
53K
c.
4359
A>G
p.
= Sy
n 1
01
BR
CA
2 11
46
64
G to
C
Ser t
o Th
r S1
479T
c.
4436
G>C
p.
Ser1
479T
hr
M
20
2 B
RC
A2
11
4789
C
to T
Le
u to
Leu
L1
521L
c.
4561
C>T
p.
= Sy
n 1
10
BR
CA
2 11
47
91
G to
A
Leu
to L
eu
L152
1L
c.45
63G
>A
p.=
Syn
52
3 B
RC
A2
11
4813
G
to A
G
ly to
Arg
G
1529
R
c.45
85G
>A
p.G
ly15
29A
rg
M
22
0
E 12
26 B
org
et al
.
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
11
4842
T
to C
Se
r to
Ser
S153
8S
c.46
14T>
C
p.=
Syn
10
1 B
RC
A2
11
4909
C
to A
H
is to
Asn
H
1561
N
c.46
81C
>A
p.H
is15
61A
sn
M
21
1 B
RC
A2
11
4995
A
to G
Pr
o to
Pro
P1
589P
c.
4767
A>G
p.
= Sy
n 1
10
BR
CA
2 11
50
42
T to
C
Val
to A
la
V16
05A
c.
4814
T>C
p.
Val
1605
Ala
M
1
01
BR
CA
2 11
50
58
G to
A
Val
to V
al
V16
10V
c.
4830
G>A
p.
= Sy
n 1
10
BR
CA
2 11
50
93
G to
C
Arg
to T
hr
R16
22T
c.48
65G
>C
p.A
rg16
22Th
r M
1
01
BR
CA
2 11
51
55
G to
A
Val
to Il
e V
1643
I c.
4927
G>A
p.
Val
1643
Ile
M
11
0 B
RC
A2
11
5248
A
to G
Se
r to
Gly
S1
674G
c.
5020
A>G
p.
Ser1
674G
ly
M
11
0 B
RC
A2
11
5279
C
to G
Th
r to
Ser
T168
4S
c.50
51C
>G
p.Th
r168
4Ser
M
1
01
BR
CA
2 11
54
19
C to
T
His
to T
yr
H17
31Y
c.
5191
C>T
p.
His
1731
Tyr
M
10
1 B
RC
A2
11
5426
C
to T
Se
r to
Phe
S173
3F
c.51
98C
>T
p.Se
r173
3Phe
M
1
10
BR
CA
2 11
54
27
C to
T
Ser t
o Se
r S1
733S
c.
5199
C>T
p.
= Sy
n 18
513
B
RC
A2
11
5547
G
to A
G
lu to
Glu
E1
773E
c.
5319
G>A
p.
= Sy
n 1
01
BR
CA
2 11
56
06
A to
G
Asn
to S
er
N17
93S
c.53
78A
>G
p.A
sn17
93Se
r M
1
01
BR
CA
2 11
56
46
A to
G
Glu
to G
lu
E180
6E
c.54
18A
>G
p.=
Syn
30
3 B
RC
A2
11
5723
C
to A
Se
r to
Tyr
S183
2Y
c.54
95C
>A
p.Se
r183
2Tyr
M
1
01
BR
CA
2 11
58
06
A to
G
Lys t
o G
lu
K18
60E
c.55
78A
>G
p.Ly
s186
0Glu
M
1
01
BR
CA
2 11
58
62
C to
G
Asn
to L
ys
N18
78K
c.
5634
C>G
p.
Asn
1878
Lys
M
22
0 B
RC
A2
11
5863
G
to A
G
lu to
Lys
E1
879K
c.
5635
G>A
p.
Glu
1879
Lys
M
11
0 B
RC
A2
11
5868
T
to G
A
sn to
Lys
N
1880
K
c.56
40T>
G
p.A
sn18
80Ly
s M
3
21
BR
CA
2 11
58
87
A to
G
Thr t
o A
la
T188
7A
c.56
59A
>G
p.Th
r188
7Ala
M
1
01
BR
CA
2 11
58
96
A to
G
Met
to V
al
M18
90V
c.
5668
A>G
p.
Met
1890
Val
M
1
01
BR
CA
2 11
59
11
G to
A
Glu
to L
ys
E189
5K
c.56
83G
>A
p.G
lu18
95Ly
s M
1
01
BR
CA
2 11
59
32
G to
A
Asp
to A
sn
D19
02N
c.
5704
G>A
p.
Asp
1902
Asn
M
1
01
BR
CA
2 11
59
72
C to
T
Thr t
o M
et
T191
5M
c.57
44C
>T
p.Th
r191
5Met
M
10
830
78
BR
CA
2 11
59
96
A to
C
Asp
to A
la
D19
23A
c.
5768
A>C
p.
Asp
1923
Ala
M
1
01
BR
CA
2 11
60
13
A to
G
Ile to
Val
I1
929V
c.
5785
A>G
p.
Ile19
29V
al
M
10
1 B
RC
A2
11
6107
G
to A
C
ys to
Tyr
C
1960
Y
c.58
79G
>A
p.C
ys19
60Ty
r M
1
10
BR
CA
2 11
61
72
A to
G
Ser t
o G
ly
S198
2G
c.59
44A
>G
p.Se
r198
2Gly
M
1
01
BR
CA
2 11
63
28
C to
T
Arg
to C
ys
R20
34C
c.
6100
C>T
p.
Arg
2034
Cys
M
21
615
B
RC
A2
11
6347
T
to A
Ile
to L
ys
I204
0K
c.61
19T>
A
p.Ile
2040
Lys
M
11
0 B
RC
A2
11
6545
T
to C
Le
u to
Pro
L2
106P
c.
6317
T>C
p.
Leu2
106P
ro
M
10
1 B
RC
A2
11
6550
C
to T
A
rg to
Cys
R
2108
C
c.63
22C
>T
p.A
rg21
08C
ys
M
21
1 B
RC
A2
11
6551
G
to A
A
rg to
His
R
2108
H
c.63
23G
>A
p.A
rg21
08H
is
M
72
5 B
RC
A2
11
6575
A
to G
H
is to
Arg
H
2116
R
c.63
47A
>G
p.H
is21
16A
rg
M
21
1 B
RC
A2
11
6640
G
to T
V
al to
Phe
V
2138
F c.
6412
G>T
p.
Val
2138
Phe
M
21
1 B
RC
A2
11
6683
C
to A
Se
r to
Tyr
S215
2Y
c.64
55C
>A
p.Se
r215
2Tyr
M
1
01
BR
CA
2 11
66
93
C to
T
Leu
to L
eu
L215
5L
c.64
65C
>T
p.=
Syn
11
0
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
27
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
11
6717
A
to G
G
ln to
Gln
Q
2163
Q
c.64
89A
>G
p.=
Syn
11
0 B
RC
A2
11
6741
C
to G
V
al to
Val
V
2171
V
c.65
13C
>G
p.=
Syn
42
2 B
RC
A2
11
6841
G
to A
V
al to
Met
V
2205
M
c.66
13G
>A
p.V
al22
05M
et
M
10
1 B
RC
A2
11
6976
A
to G
Th
r to
Ala
T2
250A
c.
6748
A>G
p.
Thr2
250A
la
M
21
1 B
RC
A2
11
7049
G
to T
G
ly to
Val
G
2274
V
c.68
21G
>T
p.G
ly22
74V
al
M
10
1 B
RC
A2
11
7069
+11
A to
G
-
IVS1
1+11
A>G
c.
6841
+11A
>G
IV
S 1
01
BR
CA
2 11
70
69+3
3 A
to G
-
IVS1
1+33
A>G
c.
6841
+33A
>G
IV
S 1
10
BR
CA
2 11
70
69+3
6 A
to G
-
IVS1
1+36
A>G
c.
6841
+36A
>G
IV
S 1
10
BR
CA
2 12
70
70-7
3 T
to A
-
IVS1
1-73
T>A
c.
6842
-73T
>A
IV
S 1
10
BR
CA
2 12
70
70-2
2 T
to A
-
IVS1
1-22
T>A
c.
6842
-22T
>A
IV
S 1
10
BR
CA
2 12
70
81
A to
G
Ile to
Val
I2
285V
c.
6853
A>G
p.
Ile22
85V
al
M
40
4 B
RC
A2
12
7149
A
to G
Se
r to
Ser
S230
7S
c.69
21A
>G
p.=
Syn
10
1 B
RC
A2
13
7171
A
to C
Ile
to L
eu
I231
5L
c.69
43A
>C
p.Ile
2315
Leu
M
10
1 B
RC
A2
13
7235
+4
A to
G
- IV
S13+
4A>G
c.
7007
+4A
>G
IV
S 1
01
BR
CA
2 13
72
35+5
2 C
to A
-
IVS1
3+52
C>A
c.
7007
+52C
>A
IV
S 1
01
BR
CA
2 14
72
36-6
2 A
to G
-
IVS1
3-62
A>G
c.
7008
-62A
>G
IV
S 1
10
BR
CA
2 14
72
45
G to
C
Lys t
o A
sn
K23
39N
c.
7017
G>C
p.
Lys2
339A
sn
M
20
2 B
RC
A2
14
7275
T
to A
Ph
e to
Leu
F2
349L
c.
7047
T>A
p.
Phe2
349L
eu
M
11
0 B
RC
A2
14
7280
C
to G
A
la to
Gly
A
2351
G
c.70
52C
>G
p.A
la23
51G
ly
M
11
0 B
RC
A2
14
7285
G
to C
G
ly to
Arg
G
2353
R
c.70
57G
>C
p.G
ly23
53A
rg
M
11
0 B
RC
A2
14
7378
C
to A
G
ln to
Lys
Q
2384
K
c.71
50C
>A
p.G
ln23
84Ly
s M
1
01
BR
CA
2 14
74
60
A to
C
Lys t
o Th
r K
2411
T c.
7232
A>C
p.
Lys2
411T
hr
M
10
1 B
RC
A2
14
7470
A
to G
Se
r to
Ser
S241
4S
c.72
42A
>G
p.=
Syn
743
245
498
BR
CA
2 14
75
47
A to
G
His
to A
rg
H24
40R
c.
7319
A>G
p.
His
2440
Arg
M
3
12
BR
CA
2 14
76
25
C to
T
Ala
to V
al
A24
66V
c.
7397
C>T
p.
Ala
2466
Val
M
3
12
BR
CA
2 14
76
41
A to
G
Thr t
o Th
r T2
471T
c.
7413
A>G
p.
= Sy
n 1
01
BR
CA
2 14
76
63+5
T
to C
-
IVS1
4+5T
>C
c.74
35+5
T>C
IVS
10
1 B
RC
A2
14
7663
+23
A to
G
- IV
S14+
23A
>G
c.74
35+2
3A>G
IVS
10
1 B
RC
A2
14
7663
+53
C to
T
-
IVS1
4+53
C>T
c.
7435
+53C
>T
IV
S 2
20
BR
CA
2 15
76
97
T to
C
Ile to
Thr
I2
490T
c.
7469
T>C
p.
Ile24
90Th
r M
11
56
BR
CA
2 15
77
78
C to
G
Thr t
o Se
r T2
517S
c.
7550
C>G
p.
Thr2
517S
er
M
10
1 B
RC
A2
15
7845
+15
A to
G
- IV
S15+
15A
>G
c.76
17+1
5A>G
IVS
10
1 B
RC
A2
15
7845
+17
C to
T
- IV
S15+
17C
>T
c.76
17+1
7C>T
IVS
10
1 B
RC
A2
16
7854
G
to A
Th
r to
Thr
T254
2T
c.76
26G
>A
p.=
Syn
20
2 B
RC
A2
16
8033
+6
C to
G
- IV
S16+
6C>G
c.
7805
+6C
>G
IV
S 2
11
BR
CA
2 17
80
34-4
0 A
to G
-
IVS1
6-40
A>G
c.
7806
-40A
>G
IV
S 4
13
BR
CA
2 17
80
34-3
9 A
to G
-
IVS1
6-39
A>G
c.
7806
-39A
>G
IV
S 1
10
BR
CA
2 17
80
34-1
4 T
to C
-
IVS1
6-14
T>C
c.
7806
-14T
>C
IV
S 11
2239
173
1
E 12
28 B
org
et al
.
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
17
8106
G
to C
Tr
p to
Cys
W
2626
C
c.78
78G
>C
p.Tr
p262
6Cys
M
1
10
BR
CA
2 17
81
07
A to
T
Ile to
Phe
I2
627F
c.
7879
A>T
p.
Ile26
27Ph
e M
1
01
BR
CA
2 17
81
42
T to
G
Phe
to L
eu
F263
8L
c.79
14T>
G
p.Ph
e263
8Leu
M
1
01
BR
CA
2 17
82
04+3
5 C
to A
-
IVS1
7+35
C>A
c.
7976
+35C
>A
IV
S 2
02
BR
CA
2 17
82
04+3
6 G
to A
-
IVS1
7+36
G>A
c.
7976
+36G
>A
IV
S 1
01
BR
CA
2 18
82
16
A to
T
Glu
to V
al
E266
3V
c.79
88A
>T
p.G
lu26
63V
al
M
10
1 B
RC
A2
18
8222
A
to G
A
sp to
Gly
D
2665
G
c.79
94A
>G
p.A
sp26
65G
ly
M
21
1 B
RC
A2
18
8255
T
to C
M
et to
Thr
M
2676
T c.
8027
T>C
p.
Met
2676
Thr
M
10
1 B
RC
A2
18
8267
A
to G
A
sp to
Gly
D
2680
G
c.80
39A
>G
p.A
sp26
80G
ly
M
10
1 B
RC
A2
18
8318
G
to A
Se
r to
Asn
S2
697N
c.
8090
G>A
p.
Ser2
697A
sn
M
11
0 B
RC
A2
18
8362
G
to A
A
sp to
Asn
D
2712
V
c.81
34G
>A
p.A
sp27
12A
sn
M
11
0 B
RC
A2
18
8377
G
to T
A
la to
Ser
A
2717
S c.
8149
G>T
p.
Ala
2717
Ser
M
63
3 B
RC
A2
18
8410
G
to A
V
al to
Ile
V27
28I
c.81
82G
>A
p.V
al27
28Ile
M
10
28
BR
CA
2 19
86
88
A to
C
Val
to V
al
V28
20V
c.
8460
A>C
p.
= Sy
n 7
34
BR
CA
2 20
87
95
A to
C
Glu
to A
la
E285
6A
c.85
67A
>C
p.G
lu28
56A
la
M
154
11
BR
CA
2 20
87
97
G to
A
Ala
to T
hr
A28
57T
c.85
69G
>A
p.A
la28
57Th
r M
1
01
BR
CA
2 20
88
60+1
4 T
to C
-
IVS2
0+14
T>C
c.
8632
+14T
>C
IV
S 1
01
BR
CA
2 20
88
60+1
43
insC
-
IVS2
0+14
3ins
C
c.86
32+1
43in
sC
IV
S 1
10
BR
CA
2 21
88
61-1
6 C
to G
-
IVS2
0-16
C>G
c.
8633
-16C
>G
IV
S 2
02
BR
CA
2 21
88
75
C to
T
Pro
to S
er
P288
3S
c.86
47C
>T
p.Pr
o288
3Ser
M
1
01
BR
CA
2 21
89
82+7
5 A
to G
-
IVS2
1+75
A>G
c.
8754
+75A
>G
IV
S 1
01
BR
CA
2 22
90
58
A to
T
Ile to
Phe
I2
944F
c.
8830
A>T
p.
Ile29
44Ph
e M
2
11
BR
CA
2 22
90
78
G to
T
Lys t
o A
sn
K29
50N
c.
8850
G>T
p.
Lys2
950A
sn
M
33
0 B
RC
A2
22
9079
G
to A
A
la to
Thr
A
2951
T c.
8851
G>A
p.
Ala
2951
Thr
M
2210
12
BR
CA
2 22
91
30
A to
C
Thr t
o Pr
o T2
968P
c.
8902
A>C
p.
Thr2
968P
ro
M
21
1 B
RC
A2
22
9133
G
to A
V
al to
Met
V
2969
M
c.89
05G
>A
p.V
al29
69M
et
M
10
1 B
RC
A2
23
9332
A
to G
Ty
r to
Cys
Y
3035
C
c.91
04A
>G
p.Ty
r303
5Cys
M
2
11
BR
CA
2 24
93
82
C to
T
Arg
to T
rp
R30
52W
c.
9154
C>T
p.
Arg
3052
Trp
M
10
1 B
RC
A2
24
9463
G
to A
V
al to
Ile
V30
79I
c.92
35G
>A
p.V
al30
79Ile
M
1
01
BR
CA
2 24
94
84+2
8 de
l T
- IV
S24+
28de
lT
c.92
56+2
8del
T
IVS
22
0 B
RC
A2
25
9485
-113
T
to G
-
IVS2
4-11
3T>G
c.
9257
-113
T>G
IVS
50
5 B
RC
A2
25
9485
-110
A
to G
-
IVS2
4-11
0A>G
c.
9257
-110
A>G
IVS
10
1 B
RC
A2
25
9485
-83
G to
A
- IV
S24-
83G
>A
c.92
57-8
3G>A
IVS
188
10
BR
CA
2 25
94
85-4
9 T
to C
-
IVS2
4-49
T>C
c.
9257
-49T
>C
IV
S 1
10
BR
CA
2 25
94
85-1
6 T
to C
-
IVS2
4-16
T>C
c.
9257
-16T
>C
IV
S 34
826
B
RC
A2
25
9520
T
to C
Ty
r to
His
Y
3098
H
c.92
92T>
C
p.Ty
r309
8His
M
1
01
BR
CA
2 25
95
29
C to
T
Leu
to L
eu
L310
1L
c.93
01C
>T
p.=
Syn
10
1 B
RC
A2
25
9594
A
to G
A
la to
Ala
A
3122
A
c.93
66A
>G
p.=
Syn
10
1
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
29
Gen
eE
xon
NT
1B
ase
Ch
AA
Cha
nge
BIC
2H
GV
3 DN
A
HG
V p
rote
in
Typ
e4T
otal
5C
BC
UB
CB
RC
A2
25
9639
T
to G
Th
r to
Thr
T313
7T
c.94
11T>
G
p.=
Syn
11
0 B
RC
A2
26
9741
A
to G
Ile
to M
et
I317
1M
c.95
13A
>G
p.Ile
3171
Met
M
1
10
BR
CA
2 26
98
34
G to
C
Pro
to P
ro
P320
2P
c.96
06G
>C
p.=
Syn
11
0 B
RC
A2
26
9876
+54
G to
A
- IV
S26+
54G
>A
c.96
48+5
4G>A
IVS
21
1 B
RC
A2
26
9876
+84
G to
A
- IV
S26+
84G
>A
c.96
48+8
4G>A
IVS
123
9 B
RC
A2
26
9876
+106
de
l T
- IV
S26+
106d
elT
c.96
48+1
06de
lT
IV
S 5
23
BR
CA
2 27
98
77-6
7 de
l TTA
C
- IV
S26-
67de
l4
c.96
49-6
7del
TTA
C
IV
S 1
01
BR
CA
2 27
98
77-1
9 G
to A
-
IVS2
6-19
G>A
c.
9649
-19G
>A
IV
S 2
02
BR
CA
2 27
99
58
G to
A
Val
to Il
e V
3244
I c.
9730
G>A
p.
Val
3244
Ile
M
21
1 B
RC
A2
27
1010
3 C
to T
Pr
o to
Leu
P3
292L
c.
9875
C>T
p.
Pro3
292L
eu
M
10
1 B
RC
A2
27
1020
4 A
to T
Ly
s to
stop
K
3326
X
c.99
76A
>T
p.Ly
s332
6X
N
409
31
BR
CA
2 27
10
273
A to
G
Thr t
o A
la
T334
9A
c.10
045A
>G
p.Th
r334
9Ala
M
1
01
BR
CA
2 27
10
323
del C
ins
11
Stop
336
9 10
323d
elC
ins1
1 c.
1009
5del
Cin
s11
p.Se
r336
6fs
F 2
11
BR
CA
2 27
10
338
G to
A
Arg
to A
rg
R33
70R
c.
1011
0G>A
p.
= Sy
n 8
35
BR
CA
2 27
10
339
A to
G
Thr t
o A
la
T337
1A
c.10
111A
>G
p.Th
r337
1Ala
M
3
03
BR
CA
2 27
10
378
C to
T
Arg
to S
top
R33
84X
c.
1015
0C>T
p.
Arg
3384
X
N
11
0 B
RC
A2
27
1043
1 G
to A
Th
r to
Thr
T340
1T
c.10
203G
>A
p.=
Syn
10
1 B
RC
A2
27
1046
2 A
to G
Ile
to V
al
I341
2V
c.10
234A
>G
p.Ile
3412
Val
M
28
1018
B
RC
A2
27
1051
6 C
to T
3'
UTR
U
AA
+31C
>T
c.*3
1C>T
UTR
1
01
1 BR
CA
1: n
ucle
otid
e nu
mbe
r acc
ordi
ng to
Gen
Ban
k U
1468
0.1.
http
://w
ww
.ncb
i.nlm
.nih
.gov
/ent
rez/
view
er.fc
gi?d
b=nu
cleo
tide&
val=
5559
31
1 BR
CA
2: n
ucle
otid
e nu
mbe
r acc
ordi
ng to
Gen
Ban
k N
M_0
0005
9.1.
http
://w
ww
.ncb
i.nlm
.nih
.gov
/ent
rez/
view
er.fc
gi?d
b=nu
cleo
tide&
val=
4502
450
2 BIC
(Bre
ast C
ance
r Inf
orm
atio
n C
ore)
. http
://re
sear
ch.n
hgri.
nih.
gov/
bic/
3 H
GV
S (H
uman
Gen
ome
Var
iatio
n So
ciet
y). h
ttp://
ww
w.h
gvs.o
rg/m
utno
men
/recs
.htm
l4 T
ype:
F=f
ram
e sh
ift, M
=mis
sens
e, S
=spl
ice
site
, N=n
onse
nse
5 Num
ber o
f obs
erva
tions
m
utat
ions
not
ear
lier d
escr
ibed
in B
IC (b
y N
ovem
ber 2
008)
E 12
30 B
org
et al
.
Supp
. Tab
le S3
. BRC
A1 an
d BR
CA2 u
nclas
sified
varia
nts f
ound
in 70
5 con
tralat
eral
and
1398
uni
later
al br
east
canc
er p
atien
ts. P
redi
ctio
n of
func
tiona
l effe
ct o
f m
issen
se va
riant
s usin
g th
e Alig
n-GV
GD p
rogr
am.
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
1 2
101-
10
T to
C
IVS1
-10T
>C
IVS
BR
CA
1 3
200-
129
G to
A
IVS2
-129
G>A
IV
S
B
RC
A1
3 20
0-55
T
to G
IV
S2-5
5T>G
IV
S
B
RC
A1
3 23
3 G
to A
K
38K
Sy
n
B
RC
A1
3 25
3 A
to C
K
45T
M
C
098
.89
30.7
5
C25
26.0
0 66
.45
C
2526
.00
66.4
5 B
RC
A1
5 25
4-53
T
to C
IV
S4-5
3T>C
IV
S
B
RC
A1
5 25
4-23
C
to T
IV
S4-2
3C>T
IV
S
B
RC
A1
5 33
1+23
T
to A
IV
S5+2
3T>A
IV
S
B
RC
A1
7 42
1-70
G
to A
IV
S6-7
0G>A
IV
S
B
RC
A1
7 43
3 A
to G
Y
105C
M
C15
120.
91
131.
30
C15
120.
91
131.
30
C
1511
7.31
13
1.30
B
RC
A1
7 54
4 C
to A
P1
42H
M
C0
353.
86
0.00
C0
226.
93
11.1
5
C0
97.5
9 11
.15
BR
CA
1 7
560+
36
del 1
4 IV
S7+3
6del
14
IVS
BR
CA
1 8
561-
34
C to
T
IVS7
-34C
>T
IVS
BR
CA
1 8
628
G to
A
R17
0Q
M
C
057
.03
0.00
C0
57.0
3 0.
00
C
056
.64
0.00
B
RC
A1
8 65
5 A
to G
Y
179C
M
C35
40.2
2 18
2.30
C35
40.2
2 18
2.30
C45
35.6
8 18
4.08
B
RC
A1
9 66
7-80
T>
C
IVS8
-80T
>C
IVS
BR
CA
1 9
667-
58
delT
IV
S8-5
8del
T IV
S
B
RC
A1
9 66
7-17
G
to T
IV
S8-1
7G>T
IV
S
B
RC
A1
9 66
7-3
del T
IV
S8-3
delT
IV
S
B
RC
A1
9 71
0 C
to T
C
197C
Sy
n
B
RC
A1
10
713-
72
A>G
IV
S9-7
2A>G
IV
S
B
RC
A1
10
713-
34
T to
C
IVS9
-34T
>C
IVS
BR
CA
1 10
76
0 A
to G
D
214G
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
271.
19
0.00
B
RC
A1
11
812
G to
A
T231
T Sy
n
B
RC
A1
11
855
T to
G
L246
V
M
C
025
1.61
0.
00
C
023
5.27
0.
00
C
030
.92
0.00
B
RC
A1
11
944
C to
T
G27
5G
Syn
BR
CA
1 11
10
67
C to
G
S316
R
M
C
022
0.50
63
.83
C
021
7.19
68
.90
C
2546
.24
83.2
3 B
RC
A1
11
1100
A
to G
T3
27T
Syn
BR
CA
1 11
11
52
G to
T
D34
5Y
M
C
010
6.33
70
.69
C
010
6.33
70
.69
C
010
6.33
70
.69
BR
CA
1 11
11
84
G to
A
K35
5K
Syn
BR
CA
1 11
11
86
A to
G
Q35
6R
M
C
025
5.29
19
.25
C
023
8.22
28
.37
C
010
1.52
28
.37
BR
CA
1 11
12
24
del G
AT
D36
9del
IF
D
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
31
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
1 11
12
56
T to
G
I379
M
M
C
012
0.48
0.
00
C
092
.35
0.00
C0
89.2
8 0.
00
BR
CA
1 11
15
75
T to
C
F486
L M
C0
225.
33
0.00
C0
212.
92
0.00
C0
212.
92
0.00
B
RC
A1
11
1605
C
to T
R
496C
M
C0
244.
95
56.6
4
C0
244.
95
56.6
4
C15
139.
47
112.
77
BR
CA
1 11
16
06
G to
A
R49
6H
M
C
024
4.95
0.
00
C
024
4.95
0.
00
C
013
9.47
0.
00
BR
CA
1 11
17
28
A to
G
N53
7D
M
C
096
.20
0.00
C0
96.2
0 0.
00
C
096
.20
0.00
B
RC
A1
11
1767
A
to C
N
550H
M
C0
151.
68
0.00
C0
118.
33
4.81
C0
79.7
9 26
.81
BR
CA
1 11
18
31
T to
C
I571
T M
C0
171.
12
0.00
C0
142.
37
0.00
C0
142.
37
0.00
B
RC
A1
11
1908
G
to A
E5
97K
M
C0
152.
38
0.00
C0
152.
38
0.00
C0
128.
69
0.00
B
RC
A1
11
1965
de
l TC
T S6
16de
l IF
D
BR
CA
1 11
19
84
C to
T
A62
2V
M
C
022
4.84
2.
03
C
022
4.84
2.
03
C
022
4.84
2.
03
BR
CA
1 11
20
30
T to
C
T637
T Sy
n
B
RC
A1
11
2090
A
to G
Q
657Q
Sy
n
B
RC
A1
11
2196
G
to A
D
693N
M
C0
176.
25
0.00
C0
176.
25
0.00
C0
170.
55
0.00
B
RC
A1
11
2201
C
to T
S6
94S
Syn
BR
CA
1 11
24
18
A to
G
S767
G
M
C
016
7.35
29
.38
C
016
7.35
29
.38
C
016
7.35
29
.38
BR
CA
1 11
24
30
T to
C
L771
L Sy
n
B
RC
A1
11
2471
G
to A
S7
84S
Syn
BR
CA
1 11
25
35
G to
A
A80
6T
M
C
025
4.20
0.
00
C
025
4.20
0.
00
C
015
5.03
0.
00
BR
CA
1 11
25
77
A to
G
K82
0E
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
026
2.85
0.
00
BR
CA
1 11
25
92
G to
T
D82
5Y
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
025
1.13
51
.67
BR
CA
1 11
25
96
C to
A
T826
K
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
021
5.31
73
.23
BR
CA
1 11
26
02
del G
CT
G82
8del
IF
D
BR
CA
1 11
26
37
A to
G
S840
G
M
C
014
4.64
28
.37
C
014
4.64
28
.37
C
012
3.92
28
.37
BR
CA
1 11
26
40
C to
T
R84
1W
M
C
1511
1.49
78
.29
C
1511
1.49
78
.29
C
1510
9.21
85
.03
BR
CA
1 11
26
41
G to
A
R84
1Q
M
C
011
1.49
0.
00
C
011
1.49
0.
00
C
010
9.21
0.
00
BR
CA
1 11
26
85
T to
C
Y85
6H
M
C
020
9.64
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AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
2 10
20
16
T to
C
D59
6D
Syn
BR
CA
2 10
20
20
A to
G
T598
A
M
C
017
0.63
0.
00
C
016
7.89
0.
00
C
014
4.64
0.
00
BR
CA
2 10
20
32
G to
A
G60
2R
M
C
017
4.09
13
.17
C
017
4.09
13
.17
C
017
0.79
13
.17
BR
CA
2 10
20
46
G to
A
P606
P Sy
n
B
RC
A2
10
2117
C
to T
T6
30I
M
C
035
3.86
0.
00
C
024
8.25
28
.78
C
020
2.47
39
.32
BR
CA
2 10
21
37+2
3 in
s T
IVS1
0+23
insT
IV
S
B
RC
A2
11
2139
T
to C
G
637G
Sy
n
B
RC
A2
11
2166
C
to T
S6
46S
Syn
BR
CA
2 11
21
92
C to
G
P655
R
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
026
1.33
13
.17
BR
CA
2 11
23
10
T to
C
N69
4N
Syn
BR
CA
2 11
24
57
T to
C
H74
3H
Syn
BR
CA
2 11
25
78
A to
G
M78
4V
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
025
8.32
0.
00
BR
CA
2 11
26
40
A to
G
E804
E Sy
n
B
RC
A2
11
2778
A
to G
Q
850Q
Sy
n
B
RC
A2
11
2937
A
to G
L9
03L
Syn
BR
CA
2 11
30
31
G to
A
D93
5N
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
027
1.19
0.
00
BR
CA
2 11
30
69
G to
T
L947
F M
C0
353.
86
0.00
C0
353.
86
0.00
C0
353.
86
0.00
B
RC
A2
11
3111
G
to A
Q
961Q
Sy
n
B
RC
A2
11
3147
G
to A
S9
73S
Syn
BR
CA
2 11
31
85
A to
G
N98
6S
M
C
035
3.86
0.
00
C
021
7.19
0.
00
C
021
7.19
0.
00
BR
CA
2 11
31
91
A to
C
D98
8A
M
C
035
3.86
0.
00
C
027
6.16
0.
00
C
027
6.16
0.
00
BR
CA
2 11
31
99
A to
G
N99
1D
M
C
035
3.86
0.
00
C
026
8.84
0.
00
C
026
6.51
0.
00
BR
CA
2 11
32
83
C to
G
L101
9V
M
C
024
6.16
0.
00
C
024
6.16
0.
00
C
024
5.67
11
.33
BR
CA
2 11
34
14
T to
C
P106
2P
Syn
BR
CA
2 11
34
44
A to
G
L107
2L
Syn
BR
CA
2 11
34
92
T to
C
P108
8P
Syn
BR
CA
2 11
36
24
A to
G
K11
32K
Sy
n
B
RC
A2
11
3645
G
to A
K
1139
K
Syn
BR
CA
2 11
36
48
T to
C
S114
0S
Syn
BR
CA
2 11
37
44
G to
A
S117
2S
Syn
BR
CA
2 11
39
45
A to
G
K12
39K
Sy
n
B
RC
A2
11
4035
T
to C
V
1269
V
Syn
BR
CA
2 11
40
42
A to
G
M12
72V
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
235.
10
0.00
B
RC
A2
11
4062
T
to C
H
1278
H
Syn
BR
CA
2 11
40
76
T to
C
V12
83A
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
246.
16
35.6
0 B
RC
A2
11
4097
G
to A
C
1290
Y
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
024
8.25
53
.70
E 12
36 B
org
et al
.
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
2 11
41
44
G to
A
V13
06I
M
C
035
3.86
0.
00
C
024
0.36
0.
00
C
096
.19
0.00
B
RC
A2
11
4289
C
to T
T1
354M
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
246.
14
46.9
3 B
RC
A2
11
4296
G
to A
L1
356L
Sy
n
B
RC
A2
11
4318
A
to C
I1
364L
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
260.
21
4.86
B
RC
A2
11
4415
A
to G
Q
1396
R
M
C
035
3.86
0.
00
C
023
3.41
39
.51
C
010
7.73
39
.51
BR
CA
2 11
44
52
G to
A
Q14
08Q
Sy
n
B
RC
A2
11
4469
C
to T
T1
414M
M
C0
261.
51
0.00
C0
261.
51
0.00
C0
261.
51
0.00
B
RC
A2
11
4486
G
to T
D
1420
Y
M
C
011
9.25
62
.47
C
011
9.25
62
.47
C
1587
.36
87.6
7 B
RC
A2
11
4587
A
to G
K
1453
K
Syn
BR
CA
2 11
46
64
G to
C
S147
9T
M
C
025
4.15
0.
00
C
025
4.15
0.
00
C
024
4.14
0.
00
BR
CA
2 11
47
89
C to
T
L152
1L
Syn
BR
CA
2 11
47
91
G to
A
L152
1L
Syn
BR
CA
2 11
48
13
G to
A
G15
29R
M
C65
0.00
12
5.13
C65
0.00
12
5.13
C65
0.00
12
5.13
B
RC
A2
11
4842
T
to C
S1
538S
Sy
n
B
RC
A2
11
4909
C
to A
H
1561
N
M
C
018
1.60
0.
00
C
016
5.75
0.
00
C
016
5.75
0.
00
BR
CA
2 11
49
95
A to
G
P158
9P
Syn
BR
CA
2 11
50
42
T to
C
V16
05A
M
C0
244.
82
0.00
C0
144.
08
1.01
C0
144.
08
1.01
B
RC
A2
11
5058
G
to A
V
1610
V
Syn
BR
CA
2 11
50
93
G to
C
R16
22T
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
035
3.86
0.
00
BR
CA
2 11
51
55
G to
A
V16
43I
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
024
2.23
0.
00
BR
CA
2 11
52
48
A to
G
S167
4G
M
C
013
8.80
0.
00
C
013
8.80
0.
00
C
013
8.80
0.
00
BR
CA
2 11
52
79
C to
G
T168
4S
M
C
017
1.12
0.
00
C
014
2.37
0.
00
C
010
3.68
0.
00
BR
CA
2 11
54
19
C to
T
H17
31Y
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
231.
11
63.2
4 B
RC
A2
11
5426
C
to T
S1
733F
M
C0
353.
86
0.00
C15
209.
54
110.
53
C
1599
.44
110.
53
BR
CA
2 11
54
27
C to
T
S173
3S
Syn
BR
CA
2 11
55
47
G to
A
E177
3E
Syn
BR
CA
2 11
56
06
A to
G
N17
93S
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
035
3.86
0.
00
BR
CA
2 11
56
46
A to
G
E180
6E
Syn
BR
CA
2 11
57
23
C to
A
S183
2Y
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
025
7.76
12
.16
BR
CA
2 11
58
06
A to
G
K18
60E
M
C
024
6.80
16
.18
C
024
4.26
16
.18
C
024
4.26
16
.18
BR
CA
2 11
58
62
C to
G
N18
78K
M
C0
262.
60
0.00
C0
170.
08
0.00
C0
170.
08
0.00
B
RC
A2
11
5863
G
to A
E1
879K
M
C0
98.1
8 0.
00
C
061
.81
0.00
C0
61.8
1 0.
00
BR
CA
2 11
58
68
T to
G
N18
80K
M
C0
112.
83
34.6
9
C0
112.
83
34.6
9
C0
111.
88
36.7
1 B
RC
A2
11
5887
A
to G
T1
887A
M
C0
353.
86
0.00
C0
255.
29
0.00
C0
144.
99
0.00
B
RC
A2
11
5896
A
to G
M
1890
V
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
023
6.57
0.
00
BR
CA
2 11
59
11
G to
A
E189
5K
M
C
035
3.86
0.
00
C
027
6.16
0.
00
C
017
6.53
0.
00
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
37
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
2 11
59
32
G to
A
D19
02N
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
213.
16
22.7
5 B
RC
A2
11
5972
C
to T
T1
915M
M
C0
353.
86
0.00
C0
258.
55
0.00
C0
162.
56
0.00
B
RC
A2
11
5996
A
to C
D
1923
A
M
C
035
3.86
0.
00
C
025
1.13
0.
00
C
015
8.16
1.
52
BR
CA
2 11
60
13
A to
G
I192
9V
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
024
2.23
0.
00
BR
CA
2 11
61
07
G to
A
C19
60Y
M
C0
353.
86
0.00
C0
255.
29
4.05
C0
225.
33
4.05
B
RC
A2
11
6172
A
to G
S1
982G
M
C0
46.2
4 50
.15
C
046
.24
50.1
5
C0
46.2
4 50
.15
BR
CA
2 11
63
28
C to
T
R20
34C
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
262.
81
11.3
3 B
RC
A2
11
6347
T
to A
I2
040K
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
353.
86
0.00
B
RC
A2
11
6545
T
to C
L2
106P
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
251.
03
0.00
B
RC
A2
11
6550
C
to T
R
2108
C
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
026
7.27
0.
00
BR
CA
2 11
65
51
G to
A
R21
08H
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
267.
27
0.00
B
RC
A2
11
6575
A
to G
H
2116
R
M
C
035
3.86
0.
00
C
025
8.33
1.
62
C
011
6.00
1.
62
BR
CA
2 11
66
40
G to
T
V21
38F
M
C
026
1.33
21
.28
C
026
1.33
21
.28
C
026
1.33
21
.28
BR
CA
2 11
66
83
C to
A
S215
2Y
M
C
022
6.57
85
.34
C
021
5.31
85
.34
C
1576
.97
92.2
5 B
RC
A2
11
6693
C
to T
L2
155L
Sy
n
B
RC
A2
11
6717
A
to G
Q
2163
Q
Syn
BR
CA
2 11
67
41
C to
G
V21
71V
Sy
n
B
RC
A2
11
6841
G
to A
V
2205
M
M
C
035
3.86
0.
00
C
023
8.68
0.
00
C
013
4.86
0.
00
BR
CA
2 11
69
76
A to
G
T225
0A
M
C
015
2.38
0.
00
C
011
4.06
0.
00
C
011
4.06
0.
00
BR
CA
2 11
70
49
G to
T
G22
74V
M
C0
257.
76
0.00
C0
160.
70
0.00
C0
160.
70
0.00
B
RC
A2
11
7069
+11
A to
G
IVS1
1+11
A>G
IV
S
B
RC
A2
11
7069
+33
A to
G
IVS1
1+33
A>G
IV
S
B
RC
A2
11
7069
+36
A to
G
IVS1
1+36
A>G
IV
S
B
RC
A2
12
7070
-73
T to
A
IVS1
1-73
T>A
IV
S
B
RC
A2
12
7070
-22
T to
A
IVS1
1-22
T>A
IV
S
B
RC
A2
12
7081
A
to G
I2
285V
M
C0
35.6
8 26
.34
C
154.
86
28.6
8
C25
0.00
28
.68
BR
CA
2 12
71
49
A to
G
S230
7S
Syn
BR
CA
2 13
71
71
A to
C
I231
5L
M
C
010
9.50
0.
00
C
010
9.50
0.
00
C
010
9.50
0.
00
BR
CA
2 13
72
35+4
A
to G
IV
S13+
4A>G
IV
S
B
RC
A2
13
7235
+52
C to
A
IVS1
3+52
C>A
IV
S
B
RC
A2
14
7236
-62
A to
G
IVS1
3-62
A>G
IV
S
B
RC
A2
14
7245
G
to C
K
2339
N
M
C
024
8.62
0.
00
C
096
.44
28.6
1
C0
96.4
4 28
.61
BR
CA
2 14
72
75
T to
A
F234
9L
M
C
026
1.25
0.
00
C
012
4.40
0.
00
C
010
8.52
0.
00
BR
CA
2 14
72
80
C to
G
A23
51G
M
C0
251.
03
0.00
C0
154.
93
28.3
7
C0
154.
93
28.3
7 B
RC
A2
14
7285
G
to C
G
2353
R
M
C
025
1.53
5.
07
C
017
0.54
5.
07
C
017
0.54
5.
07
BR
CA
2 14
73
78
C to
A
Q23
84K
M
C0
353.
86
0.00
C0
266.
79
0.00
C0
263.
90
0.00
E 12
38 B
org
et al
.
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
2 14
74
60
A to
C
K24
11T
M
C
077
.74
0.00
C0
77.7
4 0.
00
C
650.
00
77.7
4 B
RC
A2
14
7470
A
to G
S2
414S
Sy
n
B
RC
A2
14
7547
A
to G
H
2440
R
M
C
026
8.84
13
.17
C
026
3.50
13
.17
C
026
3.50
13
.17
BR
CA
2 14
76
25
C to
T
A24
66V
M
C0
353.
86
0.00
C0
353.
86
0.00
C0
353.
86
0.00
B
RC
A2
14
7641
A
to G
T2
471T
Sy
n
B
RC
A2
14
7663
+5
T to
C
IVS1
4+5T
>C
IVS
BR
CA
2 14
76
63+2
3 A
to G
IV
S14+
23A
>G
IVS
BR
CA
2 14
76
63+5
3 C
to T
IV
S14+
53C
>T
IVS
BR
CA
2 15
76
97
T to
C
I249
0T
M
C
096
.19
49.4
2
C45
14.3
0 81
.04
C
4514
.30
81.0
4 B
RC
A2
15
7778
C
to G
T2
517S
M
C0
230.
85
0.00
C0
113.
34
46.7
0
C0
90.0
0 48
.76
BR
CA
2 15
78
45+1
5 A
to G
IV
S15+
15A
>G
IVS
BR
CA
2 15
78
45+1
7 C
to T
IV
S15+
17C
>T
IVS
BR
CA
2 16
78
54
G to
A
T254
2T
Syn
BR
CA
2 16
80
33+6
C
to G
IV
S16+
6C>G
IV
S
B
RC
A2
17
8034
-40
A to
G
IVS1
6-40
A>G
IV
S
B
RC
A2
17
8034
-39
A to
G
IVS1
6-39
A>G
IV
S
B
RC
A2
17
8034
-14
T to
C
IVS1
6-14
T>C
IV
S
B
RC
A2
17
8106
G
to C
W
2626
C
M
C
650.
00
214.
36
C
650.
00
214.
36
C
650.
00
214.
36
BR
CA
2 17
81
07
A to
T
I262
7F
M
C
150.
00
21.2
8
C15
0.00
21
.28
C
150.
00
21.2
8 B
RC
A2
17
8142
T
to G
F2
638L
M
C0
21.6
1 21
.82
C
150.
00
21.8
2
C15
0.00
21
.82
BR
CA
2 17
82
04+3
5 C
to A
IV
S17+
35C
>A
IVS
BR
CA
2 17
82
04+3
6 G
to A
IV
S17+
36G
>A
IVS
BR
CA
2 18
82
16
A to
T
E266
3V
M
C
650.
00
121.
34
C
650.
00
121.
34
C
650.
00
121.
34
BR
CA
2 18
82
22
A to
G
D26
65G
M
C65
0.00
93
.77
C
650.
00
93.7
7
C65
0.00
93
.77
BR
CA
2 18
82
55
T to
C
M26
76T
M
C
092
.35
0.00
C0
92.3
5 0.
00
C
092
.35
0.00
B
RC
A2
18
8267
A
to G
D
2680
G
M
C
1544
.60
75.3
3
C15
44.6
0 75
.33
C
1544
.60
75.3
3 B
RC
A2
18
8318
G
to A
S2
697N
M
C0
82.6
7 0.
00
C
082
.67
0.00
C0
82.6
7 0.
00
BR
CA
2 18
83
62
G to
A
D27
12V
M
C0
152.
33
55.0
5
C0
114.
13
71.4
1
C0
112.
66
71.4
4 B
RC
A2
18
8377
G
to T
A
2717
S M
C0
134.
90
2.75
C0
133.
94
2.75
C0
133.
94
2.75
B
RC
A2
18
8410
G
to A
V
2728
I M
C0
28.6
8 0.
00
C
028
.68
0.00
C0
28.6
8 0.
00
BR
CA
2 19
86
88
A to
C
V28
20V
Sy
n
B
RC
A2
20
8795
A
to C
E2
856A
M
C0
171.
12
0.00
C0
133.
09
0.00
C0
106.
71
0.00
B
RC
A2
20
8797
G
to A
A
2857
T M
C0
245.
92
0.00
C0
241.
18
0.00
C0
241.
18
0.00
B
RC
A2
20
8860
+14
T to
C
IVS2
0+14
T>C
IV
S
B
RC
A2
20
8860
+143
in
sC
IVS2
0+14
3ins
C
IVS
BR
CA
2 21
88
61-1
6 C
to G
IV
S20-
16C
>G
IVS
BRCA
1 and
BRC
A2 S
eque
nce V
arian
ts in
Uni
later
al an
d Bi
later
al Br
east
Can
cer
E 12
39
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
2 21
88
75
C to
T
P288
3S
M
C
013
9.14
36
.40
C
011
3.69
36
.40
C
011
3.69
36
.40
BR
CA
2 21
89
82+7
5 A
to G
IV
S21+
75A
>G
IVS
BR
CA
2 22
90
58
A to
T
I294
4F
M
C
04.
86
21.2
8
C0
4.86
21
.28
C
04.
86
21.2
8 B
RC
A2
22
9078
G
to T
K
2950
N
M
C
3526
.00
79.2
4
C35
26.0
0 79
.24
C
650.
00
93.8
8 B
RC
A2
22
9079
G
to A
A
2951
T M
C0
99.1
3 29
.38
C
550.
00
58.0
2
C55
0.00
58
.02
BR
CA
2 22
91
30
A to
C
T296
8P
M
C
037
.56
0.00
C0
37.5
6 0.
00
C
037
.56
0.00
B
RC
A2
22
9133
G
to A
V
2969
M
M
C
030
.92
0.00
C15
0.00
20
.52
C
150.
00
20.5
2 B
RC
A2
23
9332
A
to G
Y
3035
C
M
C
5521
.61
191.
71
C
5521
.61
191.
71
C
5521
.61
191.
71
BR
CA
2 24
93
82
C to
T
R30
52W
M
C65
0.00
10
1.29
C65
0.00
10
1.29
C65
0.00
10
1.29
B
RC
A2
24
9463
G
to A
V
3079
I M
C0
28.6
8 0.
00
C
028
.68
0.00
C0
28.6
8 0.
00
BR
CA
2 24
94
84+2
8 de
l T
IVS2
4+28
delT
IV
S
B
RC
A2
25
9485
-113
T
to G
IV
S24-
113T
>G
IVS
BR
CA
2 25
94
85-1
10
A to
G
IVS2
4-11
0A>G
IV
S
B
RC
A2
25
9485
-83
G to
A
IVS2
4-83
G>A
IV
S
B
RC
A2
25
9485
-49
T to
C
IVS2
4-49
T>C
IV
S
B
RC
A2
25
9485
-16
T to
C
IVS2
4-16
T>C
IV
S
B
RC
A2
25
9520
T
to C
Y
3098
H
M
C
015
2.53
0.
00
C
012
0.91
0.
00
C
010
5.60
0.
00
BR
CA
2 25
95
29
C to
T
L310
1L
Syn
BR
CA
2 25
95
94
A to
G
A31
22A
Sy
n
B
RC
A2
25
9639
T
to G
T3
137T
Sy
n
B
RC
A2
26
9741
A
to G
I3
171M
M
C0
185.
64
0.00
C0
181.
93
0.00
C0
181.
93
0.00
B
RC
A2
26
9834
G
to C
P3
202P
Sy
n
B
RC
A2
26
9876
+54
G to
A
IVS2
6+54
G>A
IV
S
B
RC
A2
26
9876
+84
G to
A
IVS2
6+84
G>A
IV
S
B
RC
A2
26
9876
+106
de
l T
IVS2
6+10
6del
T IV
S
B
RC
A2
27
9877
-67
del T
TAC
IV
S26-
67de
l4
IVS
BR
CA
2 27
98
77-1
9 G
to A
IV
S26-
19G
>A
IVS
BR
CA
2 27
99
58
G to
A
V32
44I
M
C
023
4.51
0.
00
C
016
9.82
0.
00
C
016
9.82
0.
00
BR
CA
2 27
10
103
C to
T
P329
2L
M
C
075
.14
62.6
8
C0
75.1
4 62
.68
C
075
.14
62.6
8 B
RC
A2
27
1020
4 A
to T
K
3326
X
N
BR
CA
2 27
10
273
A to
G
T334
9A
M
C
550.
00
58.0
2
C55
0.00
58
.02
C
550.
00
58.0
2 B
RC
A2
27
1032
3 de
l C in
s 11
1032
3del
Cin
s11
F
B
RC
A2
27
1033
8 G
to A
R
3370
R
Syn
BR
CA
2 27
10
339
A to
G
T337
1A
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
021
5.24
0.
00
BR
CA
2 27
10
378
C to
T
R33
84X
N
B
RC
A2
27
1043
1 G
to A
T3
401T
Sy
n
E 12
40 B
org
et al
.
A
GV
GD
4 Sea
urc
hin
A
GV
GD
Puf
ferf
ish
AG
VG
D X
enop
us
Gen
eE
xon
NT
1B
ase
Ch
BIC
2T
ype3
Cla
ss5
GV
GD
Cla
ssG
VG
DC
lass
GV
GD
BR
CA
2 27
10
462
A to
G
I341
2V
M
C
035
3.86
0.
00
C
035
3.86
0.
00
C
024
4.82
0.
00
BR
CA
2 27
10
516
C to
T
UTR
U
TR
1 BR
CA
1: n
ucle
otid
e nu
mbe
r acc
ordi
ng to
Gen
Ban
k U
1468
0.1.
http
://w
ww
.ncb
i.nlm
.nih
.gov
/ent
rez/
view
er.fc
gi?d
b=nu
cleo
tide&
val=
5559
31
1 BR
CA
2: n
ucle
otid
e nu
mbe
r acc
ordi
ng to
Gen
Bank
NM
_000
059.
1. h
ttp://
ww
w.n
cbi.n
lm.n
ih.g
ov/e
ntre
z/vi
ewer
.fcgi
?db=
nucl
eotid
e&va
l=45
0245
0 2 B
IC (B
reas
t Can
cer I
nfor
mat
ion
Cor
e). h
ttp://
rese
arch
.nhg
ri.ni
h.go
v/bi
c/ .
HG
VS
nom
encl
atur
e in
Sup
p. T
able
S2.
3 T
ype:
F=f
ram
e sh
ift, M
=mis
sens
e, N
=non
sens
e, S
yn=S
ynon
ymou
s, IF
D=i
n fr
ame
dele
tion,
IVS=
inte
rven
ing
sequ
ence
, UTR
=unt
rans
late
d re
gion
4 A
lign
Gra
ntha
m V
aria
tion
and
Gra
ntha
m D
evia
tion
(AG
VG
D)
scor
es (
of O
ctob
er 2
008)
http
://ag
vgd.
iarc
.fr,
alig
ned
dow
n to
sea
urc
hin
(Stro
ngyl
ocen
trotu
s pu
rpur
atus
), pu
ffer
fish
(Tet
raod
on n
igro
virid
is) o
r fro
g (X
enop
us la
evis
) 5 A
-GV
GD
gra
ded
clas
sifie
rs, o
rder
ed fr
om m
ost l
ikel
y to
inte
rfer
e w
ith fu
nctio
n to
leas
t lik
ely:
GD
>=65
+Tan
(10)
x(G
V^2
.5) =
> C
lass
C65
<=>
mos
t lik
ely
GD
>=55
+Tan
(10)
x(G
V^2
.0) =
> C
lass
C55
G
D>=
45+T
an(1
5)x(
GV
^1.7
) =>
Cla
ss C
45
GD
>=35
+Tan
(50)
x(G
V^1
.1) =
> C
lass
C35
G
D>=
25+T
an(5
5)x(
GV
^0.9
5) =
> C
lass
C25
G
D>=
15+T
an(7
5)x(
GV
^0.6
) =>
Cla
ss C
15
Else
(GD
<15+
Tan(
75)x
(GV
^0.6
)) =
> C
lass
C0
<=>
less
like
ly