PMID: 26023681

Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic.

EBioMedicine
SB Foley, JJ Rios, VE Mgbemena, LS Robinson, HL Hampel, AE Toland, L Durham, TS Ross
2015-01

180 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
13-32945142-GAG-G BRCA2 c.8537_8538delAG p.Glu2846Glyfs*22 Frameshift 20/27 -
19-11210928-C-T LDLR c.97C>T p.Gln33* Nonsense 2/18 -
13-32914137-C-G BRCA2 c.5645C>G p.Ser1882* Nonsense 11/27 -
13-32914137-C-A BRCA2 c.5645C>A p.Ser1882* Nonsense 11/27 -
13-32911304-AGCAA-A BRCA2 c.2812_2815delGCAA p.Ala938Profs*21 Frameshift 11/27 -
7-6026532-T-C PMS2 c.1864A>G p.Met622Val Missense 11/15 -
19-44058885-GCG-TGA XRCC1 c.325_327delCGCinsTGA p.Arg109* Nonsense 4/17 -
1-241675397-T-TCA FH c.424_425insTG p.Gln142Leufs*11 Frameshift 4/10 -
17-41245410-G-C BRCA1 c.2138C>G p.Ser713* Nonsense 10/23 -
17-41215920-G-T BRCA1 c.5123C>A p.Ala1708Glu Missense 17/23 -
19-39001298-A-G RYR1 c.9001-2A>G - IntronicSNV - 59/105
19-11217275-C-A LDLR c.729C>A p.Cys243* Nonsense 5/18 -
7-6017260-G-A PMS2 c.2404C>T p.Arg802* Nonsense 14/15 -
3-52437508-ACG-TGA BAP1 c.1651_1653delCGTinsTGA p.Arg551* Nonsense 13/17 -
13-32954279-A-AA BRCA2 c.9253_9253dupA p.Thr3085Asnfs*26 Frameshift 24/27 -
X-32429928-G-A DMD c.4174C>T p.Gln1392* Nonsense 30/79 -
4-994779-T-C IDUA c.493+2T>C - IntronicSNV - 4/13
5-112111412-GA-G APC c.509delA p.Asp170Valfs*5 Frameshift 5/16 -
2-48028159-AAAGAA-A MSH6 c.3037_3041delAAGAA p.Lys1013Valfs*3 Frameshift 4/10 -
7-142458451-A-T PRSS1 c.86A>T p.Asn29Ile Missense 2/5 -
13-32912776-T-TT BRCA2 c.4284_4284dup p.Gln1429Serfs*9 Frameshift 11/27 -
13-32914174-C-A BRCA2 c.5682C>A p.Tyr1894* Nonsense 11/27 -
7-116423497-C-T MET c.3772C>T p.Gln1258* Nonsense 19/21 -
13-32907447-C-G BRCA2 c.1832C>G p.Ser611* Nonsense 10/27 -
13-32907447-C-A BRCA2 c.1832C>A p.Ser611* Nonsense 10/27 -
13-32968972-CC-C BRCA2 c.9403delC p.Leu3135Phefs*28 Frameshift 25/27 -
7-116339787-A-T MET c.649A>T p.Arg217* Nonsense 2/21 -
13-32912414-G-T BRCA2 c.3922G>T p.Glu1308* Nonsense 11/27 -
13-32945137-AAA-A BRCA2 c.8532_8533delAA p.Glu2846Glyfs*22 Frameshift 20/27 -
3-14177409-G-A TMEM43 c.882+1G>A - IntronicSNV - 10/11
17-41243921-T-TT BRCA1 c.3627dupA p.Glu1210Argfs*9 Frameshift 10/23 -
4-55573414-G-A KIT c.1076G>A p.Trp359* Nonsense 6/21 -
13-32900274-AAA-A BRCA2 c.462_463delAA p.Asp156*fs*1 Frameshift 5/27 -
13-32968951-C-T BRCA2 c.9382C>T p.Arg3128* Nonsense 25/27 -
13-32912365-AA-A BRCA2 c.3873delA p.Gln1291Hisfs*2 Frameshift 11/27 -
16-3779115-T-C CREBBP c.5933A>G p.Asn1978Ser Missense 31/31 -
13-32910421-TG-T BRCA2 c.1929delG p.Arg645Glufs*15 Frameshift 11/27 -
2-48026827-TTT-T MSH6 c.1705_1706delTT p.Phe569Hisfs*7 Frameshift 4/10 -
1-169500131-G-A F5 c.5101C>T p.Gln1701* Nonsense 15/25 -
13-32914885-AA-A BRCA2 c.6393delA p.Lys2131Asnfs*6 Frameshift 11/27 -
3-14175291-AG-TA TMEM43 c.565_566delAGinsTA p.Arg189* Nonsense 7/12 -
13-32914936-T-TT BRCA2 c.6444_6444dupT p.Ile2149Tyrfs*2 Frameshift 11/27 -
10-43601927-G-A RET c.971G>A p.Trp324* Nonsense 5/20 -
17-41244546-TT-T BRCA1 c.3005delA p.Asn1002Thrfs*22 Frameshift 10/23 -
4-55573415-G-A KIT c.1077G>A p.Trp359* Nonsense 6/21 -
13-32913428-AGAAA-A BRCA2 c.4936_4939delGAAA p.Glu1646Glnfs*23 Frameshift 11/27 -
17-41219631-T-A BRCA1 c.5068A>T p.Lys1690* Nonsense 16/23 -
13-32932023-CA-C BRCA2 c.7762delA p.Ile2588Tyrfs*60 Frameshift 16/27 -
13-32968854-C-G BRCA2 c.9285C>G p.Asp3095Glu Missense 25/27 -
13-32913841-A-AT BRCA2 c.5349_5350insT p.Asn1784*fs*1 Nonsense 11/27 -
13-32907415-T-A BRCA2 c.1800T>A p.Tyr600* Nonsense 10/27 -
17-41244464-A-AA BRCA1 c.3084dupT p.Asn1029*fs*1 Nonsense 10/23 -
13-32914882-T-TT BRCA2 c.6390dupT p.Lys2131*fs*1 Nonsense 11/27 -
7-116339141-G-A MET c.3G>A p.Met1Ile Missense 2/21 -
4-996536-G-A IDUA c.1206G>A p.Trp402* Nonsense 9/14 -
1-169555556-GCT-TGA F5 c.67_69delAGCinsTGA p.Ser23* Nonsense 1/25 -
13-32900277-A-AT BRCA2 c.465_466insT p.Asp156*fs*1 Nonsense 5/27 -
13-32913843-A-AA BRCA2 c.5351dupA p.Asn1784Lysfs*3 Frameshift 11/27 -
7-116339140-T-C MET c.2T>C p.Met1Thr Missense 2/21 -
11-108137933-A-AA ATM c.2502dupA p.Val835Serfs*7 Frameshift 17/63 -
17-41276047-C-A BRCA1 c.67G>T p.Glu23* Nonsense 2/23 -
22-29121230-C-T CHEK2 c.573+1G>A - IntronicSNV - 4/15
13-32914435-A-AT BRCA2 c.5943_5944insT p.Ser1982*fs*1 Nonsense 11/27 -
9-22008850-C-A CDKN2B c.103G>T p.Glu35* Nonsense 1/2 -
13-32937506-G-C BRCA2 c.8167G>C p.Asp2723His Missense 18/27 -
4-996535-G-A IDUA c.1205G>A p.Trp402* Nonsense 9/14 -
17-41244454-CTAATGTTATTA-C BRCA1 c.3084_3094del11 p.Asn1029Argfs*5 Frameshift 10/23 -
13-32913427-AA-A BRCA2 c.4935delA p.Glu1646Lysfs*24 Frameshift 11/27 -
13-32913457-C-G BRCA2 c.4965C>G p.Tyr1655* Nonsense 11/27 -
13-32913457-C-A BRCA2 c.4965C>A p.Tyr1655* Nonsense 11/27 -
3-10183536-C-T VHL c.5C>T p.Pro2Leu Missense 1/3 -
10-43601928-G-A RET c.972G>A p.Trp324* Nonsense 5/20 -
13-32905127-A-AT BRCA2 c.753_754insT p.Asp252*fs*1 Nonsense 9/27 -
17-7579710-T-A TP53 c.86A>T p.Asn29Ile Missense 3/11 -
7-75221381-CT-TA HIP1 c.376_377delAGinsTA p.Arg126* Nonsense 4/31 -
13-32932022-TCATACCCTCCAATGATGGAAAGGCT-T BRCA2 c.7761_7785del25 p.Ile2588Glufs*52 Frameshift 16/27 -
13-32920970-ATAAA-A BRCA2 c.6944_6947delTAAA p.Ile2315Lysfs*12 Frameshift 13/27 -
19-11216248-C-A LDLR c.666C>A p.Cys222* Nonsense 4/18 -
12-111352080-T-A MYL2 c.184A>T p.Lys62* Nonsense 4/7 -
13-32905142-A-AT BRCA2 c.768_769insT p.Asn257*fs*1 Nonsense 9/27 -
13-32937636-AC-A BRCA2 c.8297delC p.Thr2766Asnfs*11 Frameshift 18/27 -
7-116398532-G-T MET c.2122G>T p.Glu708* Nonsense 9/21 -
19-44058920-C-A XRCC1 c.292G>T p.Glu98* Nonsense 4/17 -
5-112177050-CG-C APC c.5759delG p.Arg1920Glnfs*50 Frameshift 16/16 -
13-32907428-A-AA BRCA2 c.1813dupA p.Ile605Asnfs*11 Frameshift 10/27 -
13-32953463-A-G BRCA2 c.8764A>G p.Ser2922Gly Missense 22/27 -
6-7570770-A-T DSP c.1675A>T p.Lys559* Nonsense 13/24 -
1-45799171-T-A MUTYH c.253A>T p.Arg85* Nonsense 3/16 -
17-41276048-T-TT BRCA1 c.66dupA p.Glu23Argfs*18 Frameshift 2/23 -
13-32914574-AGAAGA-A BRCA2 c.6082_6086delGAAGA p.Glu2028Lysfs*19 Frameshift 11/27 -
5-131911581-ACAGA-A RAD50 c.326_329delCAGA p.Thr109Asnfs*20 Frameshift 3/25 -
10-43595905-A-G RET c.74-2A>G - IntronicSNV - 1/19
13-32945140-GAGAG-G BRCA2 c.8535_8538delAGAG p.Glu2846Lysfs*16 Frameshift 20/27 -
1-25883730-A-AA LDLRAP1 c.431dupA p.His144Glnfs*27 Frameshift 4/9 -
13-32905129-GA-G BRCA2 c.755delA p.Asp252Alafs*25 Frameshift 9/27 -
13-32913427-A-AT BRCA2 c.4935_4936insT p.Glu1646*fs*1 Nonsense 11/27 -
13-32914574-AGA-A BRCA2 c.6082_6083delGA p.Glu2028Argfs*20 Frameshift 11/27 -
13-32907369-AA-A BRCA2 c.1754delA p.Lys585Argfs*29 Frameshift 10/27 -
7-116339139-A-G MET c.1A>G p.Met1Val Missense 2/21 -
3-37070382-T-C MLH1 c.1517T>C p.Val506Ala Missense 13/19 -
13-32936722-A-G BRCA2 c.7868A>G p.His2623Arg Missense 17/27 -
7-150644131-CG-TA KCNH2 c.3163_3164delCGinsTA p.Arg1055* Nonsense 14/15 -
17-41243800-C-A BRCA1 c.3748G>T p.Glu1250* Nonsense 10/23 -
13-32913565-A-AA BRCA2 c.5073_5073dupA p.Trp1692Metfs*3 Frameshift 11/27 -
17-41244496-T-TA BRCA1 c.3051_3052insT p.Asn1018*fs*1 Nonsense 10/23 -
13-32953603-CC-C BRCA2 c.8904delC p.Val2969Cysfs*7 Frameshift 22/27 -
13-32900278-AGA-A BRCA2 c.466_467delGA p.Asp156*fs*1 Frameshift 5/27 -
13-32914897-ACTTAA-A BRCA2 c.6405_6409delCTTAA p.Asn2135Lysfs*3 Frameshift 11/27 -
7-117243623-A-T CFTR c.2695A>T p.Arg899* Nonsense 17/27 -
19-11218112-G-T LDLR c.862G>T p.Glu288* Nonsense 6/18 -
1-55527230-G-A PCSK9 c.1863+1G>A - IntronicSNV - 11/11
17-41243680-T-A BRCA1 c.3868A>T p.Lys1290* Nonsense 10/23 -
13-32914767-CTT-C BRCA2 c.6275_6276delTT p.Leu2092Profs*7 Frameshift 11/27 -
13-32911278-T-TT BRCA2 c.2786dupT p.Leu929Phefs*7 Frameshift 11/27 -
7-75216097-T-A HIP1 c.439A>T p.Arg147* Nonsense 5/31 -
14-75483857-ACG-TGA MLH3 c.4216_4218delCGTinsTGA p.Arg1406* Nonsense 12/12 -
X-32563319-G-A DMD c.2125C>T p.Gln709* Nonsense 17/79 -
13-32912339-TGT-T BRCA2 c.3847_3848delGT p.Val1283Lysfs*2 Frameshift 11/27 -
5-131893019-G-A RAD50 c.3G>A p.Met1Ile Missense 1/25 -
13-32905129-GACAG-G BRCA2 c.755_758delACAG p.Asp252Valfs*24 Frameshift 9/27 -
17-41244544-T-TA BRCA1 c.3003_3004insT p.Asn1002*fs*1 Nonsense 10/23 -
13-32968854-C-A BRCA2 c.9285C>A p.Asp3095Glu Missense 25/27 -
1-169528390-C-A F5 c.730+1G>T - IntronicSNV - 5/24
13-32954050-G-C BRCA2 c.9117G>C p.Pro3039Pro Synonymous 23/27 -
13-32954050-G-A BRCA2 c.9117G>A p.Pro3039Pro Synonymous 23/27 -
13-32954050-G-T BRCA2 c.9117G>T p.Pro3039Pro Synonymous 23/27 -
13-32914192-A-AT BRCA2 c.5700_5701insT p.Glu1901*fs*1 Nonsense 11/27 -
19-11211012-G-T LDLR c.181G>T p.Glu61* Nonsense 2/18 -
13-32914356-C-A BRCA2 c.5864C>A p.Ser1955* Nonsense 11/27 -
13-32914356-C-G BRCA2 c.5864C>G p.Ser1955* Nonsense 11/27 -
13-32913731-A-AT BRCA2 c.5239_5240insT p.Asn1747Ilefs*8 Frameshift 11/27 -
17-41243611-G-A BRCA1 c.3937C>T p.Gln1313* Nonsense 10/23 -
17-41244370-C-A BRCA1 c.3178G>T p.Glu1060* Nonsense 10/23 -
1-169511717-C-A F5 c.2611G>T p.Glu871* Nonsense 13/25 -
1-201009093-GTTGCCATG-G CACNA1S c.5483_5490delTGGCAACA p.Met1828Argfs*74 Frameshift 44/44 -
13-32945140-A-AT BRCA2 c.8535_8536insT p.Glu2846*fs*1 Nonsense 20/27 -
19-44056171-GAG-TAA XRCC1 c.1078_1080delCTCinsTAA p.Leu360* Nonsense 9/17 -
19-44079608-C-T XRCC1 c.3G>A p.Met1Ile Missense 1/17 -
13-32905145-ATCAAA-A BRCA2 c.771_775delTCAAA p.Asn257Lysfs*17 Frameshift 9/27 -
13-32907370-AGAAAA-A BRCA2 c.1755_1759delGAAAA p.Lys585Asnfs*3 Frameshift 10/27 -
7-142459725-AG-TA PRSS1 c.301_302delAGinsTA p.Arg101* Nonsense 3/5 -
13-32913730-CT-C BRCA2 c.5238delT p.Asn1747Thrfs*30 Frameshift 11/27 -
13-32914174-C-G BRCA2 c.5682C>G p.Tyr1894* Nonsense 11/27 -
13-32914574-G-T BRCA2 c.6082G>T p.Glu2028* Nonsense 11/27 -
13-52542702-C-A ATP7B c.1585G>T p.Glu529* Nonsense 4/21 -
13-32914894-T-TT BRCA2 c.6402dupT p.Asn2135*fs*1 Nonsense 11/27 -
13-32911297-ATAAA-A BRCA2 c.2805_2808delTAAA p.Ala938Profs*21 Frameshift 11/27 -
13-32893291-G-T BRCA2 c.145G>T p.Glu49* Nonsense 3/27 -
13-32905130-ACAGT-A BRCA2 c.756_759delCAGT p.Asp252Glufs*24 Frameshift 9/27 -
17-41243920-C-CA BRCA1 c.3627_3628insT p.Glu1210*fs*1 Nonsense 10/23 -
13-32907367-A-AT BRCA2 c.1752_1753insT p.Lys585*fs*1 Nonsense 10/27 -
13-32911300-AACAA-A BRCA2 c.2808_2811delACAA p.Ala938Profs*21 Frameshift 11/27 -
7-116418931-C-T MET c.3442C>T p.Arg1148* Nonsense 17/21 -
6-7572197-CGC-TGA DSP c.2026_2028delCGCinsTGA p.Arg676* Nonsense 15/24 -
13-32936767-TTTCCT-T BRCA2 c.7913_7917delTTCCT p.Phe2638*fs*1 Frameshift 17/27 -
X-31947724-G-A DMD c.6901C>T p.Gln2301* Nonsense 47/79 -
7-150654439-ACG-TGA KCNH2 c.1066_1068delCGTinsTGA p.Arg356* Nonsense 5/15 -
11-94219089-C-A MRE11 c.314+1G>T - IntronicSNV - 4/19
13-32911691-TA-T BRCA2 c.3199delA p.Thr1067Leufs*10 Frameshift 11/27 -
17-41244208-C-A BRCA1 c.3340G>T p.Glu1114* Nonsense 10/23 -
13-32907026-G-T BRCA2 c.1411G>T p.Glu471* Nonsense 10/27 -
X-32486693-GCG-TGA DMD c.3082_3084delCGCinsTGA p.Arg1028* Nonsense 23/79 -
3-37045965-G-A MLH1 c.380G>A p.Arg127Lys Missense 4/19 -
17-41244464-TA-T BRCA1 c.3084delT p.Asn1029Ilefs*19 Frameshift 10/23 -
13-32913534-GTG-G BRCA2 c.5042_5043delTG p.Val1681Glufs*7 Frameshift 11/27 -
1-55505718-G-A PCSK9 c.207+1G>A - IntronicSNV - 1/11
13-32914570-CAA-C BRCA2 c.6078_6079delAA p.Glu2028Argfs*20 Frameshift 11/27 -
13-32914401-C-A BRCA2 c.5909C>A p.Ser1970* Nonsense 11/27 -
5-131977904-C-T RAD50 c.3787C>T p.Gln1263* Nonsense 25/25 -
13-32910424-A-AT BRCA2 c.1932_1933insT p.Arg645*fs*1 Nonsense 11/27 -
2-48027853-C-T MSH6 c.2731C>T p.Arg911* Nonsense 4/10 -
13-32937348-C-T BRCA2 c.8009C>T p.Ser2670Leu Missense 18/27 -
17-41256138-C-T BRCA1 c.441+1G>A - IntronicSNV - 6/22
7-75185470-C-A HIP1 c.1687G>T p.Glu563* Nonsense 18/31 -
13-32953577-C-T BRCA2 c.8878C>T p.Gln2960* Nonsense 22/27 -
7-116339220-G-T MET c.82G>T p.Glu28* Nonsense 2/21 -
13-32968940-A-T BRCA2 c.9371A>T p.Asn3124Ile Missense 25/27 -
13-32913730-T-TT BRCA2 c.5238_5238dupT p.Asn1747*fs*1 Nonsense 11/27 -
13-32954180-C-T BRCA2 c.9154C>T p.Arg3052Trp Missense 24/27 -
13-32929059-TCT-T BRCA2 c.7069_7070delCT p.Leu2357Valfs*2 Frameshift 14/27 -