Silent mutations in medical genetics databases like ClinVar contain extra value if analyzed with the most current genomics tools. In most cases the silent mutations are of low priority in big data genomics analysis, unless additional value like them being found at functionally important DNA sequences accompanies them. This presentation describes a method to add value to the silent mutations in human exome. Specifically, mapping variants, including silent variants to the known exon-intron boundaries identifies the silent mutations whose potential as pathogenic would otherwise be a lot more unclear.

1. Mehis Pold, MD
Email:mehisp@hotmail.com
1
THEY AREN’T PERFECT! WIDELY USED GENOMICS
DATABASES THAT IS…DIG DEEP!
By Mehis Pold, MD
Public databases have become one of the most used sources for information in
genomics data analysis. They too, as anything else in this world aren’t perfect
though. Case in point – ClinVar.
I mapped all ClinVar GRCh37 single nucleotide variants using my UVM (Universal
Variation Mapping) tools to known exon-intron boundaries as provided by CCDS. My
particular interest was to find ClinVar variants annotated as silent mutations but
located at conserved positions on splice junctions (see below, Fig. 1). A silent
mutation found at a conserved position of an exon-intron boundary is certainly of
higher value for interpretation of genetic finding than just a silent mutation
anywhere else on an exon. In brief, I was curious if I could add value to the silent
variants described in ClinVar.
RESULT: I found a total of 2,426 GRCh37 variants in ClinVar not annotated for
conserved splice junction positions. Out of these 2,426 variants, 159 were
annotated as silent mutations (please see below, Table 1 and 2 for more descriptive
details). For me in particular, the silent mutations on BRCA1 and BRCA2 stood out.
CONCLUSION: Anyone using public databases still needs additional tools in order
to uncover the full value found therein. Just relying on the annotations provided in
the public databases will result in overlooking important details.
Figure 1. Mapping was carried out to conserved positions on exon-intron
boundaries. E – exon, I – intron, 1 – first position, 2 –second position, z – last
position, y – second last position.
Ez I1 I2 Iy Iz E1
+1 -1 -2 -2 -1 +1
DONOR SITE ACCEPTOR SITE
Exon Intron Exon
Conserved positions

2. Mehis Pold, MD
Email:mehisp@hotmail.com
2
Table 1. Summary of ClinVar variant mapping to the known exon-intron
boundaries as provided by CCDS.
Total number of entries annotated as CRCh37: 97,811
Variants, no annotation to splice junction: 2426/97,811 = 2.5%
Silent coding region variants, no annotation to splice junction: 159/97,811 =
0.16%
Location on
splice
junction
Number of
hits in
ClinVar
Number of hits
with ClinVar silent
mutation
Splice junction description key
E1_A_MINUS 166 19 E1 - first base on exon
E1_A_PLUS 191 22 Ez - last base on exon
Ez_D_MINUS 245 39 I1 - first base on intron
Ez_D_PLUS 246 73 I2 - second base on intron
I1_D_MINUS 309 3 Iy - second last base on intron
I1_D_PLUS 315 0 Iz - last base on intron
I2_D_MINUS 92 1 A - acceptor
I2_D_PLUS 140 2 D - donor
Iy_A_MINUS 154 0 MINUS - minus strand
Iy_A_PLUS 175 0 PLUS - plus strand
Iz_A_MINUS 178 0
Iz_A_PLUS 215 0
TOTALS 2426 159
Source file: ClinVar database, variant summary, downloaded 06242014
Genome assembly - CRCh37
Variant type: single nucleotide variant
Source for exon-Intron boundary coordinates: CCDS
Table 2. The list of ClinVar silent mutations mapping to the conserved positions on
exon-intron boundaries.
E1_A_MINUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
AGA:c.699C>T (p.Gly233Gly=) AGA not provided 4:178355643
ATP4A:c.2007G>A (p.Lys669Lys=) ATP4A not provided 19:36046492
COBL:c.246C>T (p.Ser82Ser=) COBL not provided 7:51261286
MMP1:c.351G>A (p.Arg117Arg=) MMP1 not provided 11:102667893
MYH1:c.4182G>A (p.Lys1394Lys=) MYH1 not provided 17:10401234
NLRP13:c.2958G>A (p.Gly986=) NLRP13 not provided 19:56407485
NPHP3:c.1986G>A (p.Arg662=) NPHP3 Benign 3:132416206
PDE4C:c.243C>T (p.Arg81Arg=) PDE4C not provided 19:18333133

3. Mehis Pold, MD
Email:mehisp@hotmail.com
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PNKP:c.579G>A (p.Arg193=) PNKP Uncertain significance 19:50367493
POTEF:c.522G>A (p.Arg174Arg=) POTEF not provided 2:130872901
PTPRD:c.2263C>T (p.Leu755Leu=) PTPRD not provided 9:8465675
PTPRT:c.2343G>A (p.Leu781Leu=) PTPRT not provided 20:40828028
STRA6:c.114G>A (p.Gly38Gly=) STRA6 not provided 15:74490159
TMPRSS3:c.783C>T (p.Asp261=) TMPRSS3 Likely benign 21:43802343
TSC1:c.1998G>A (p.Lys666Lys=) TSC1 not provided 9:135779841
TSC1:c.738G>A (p.Arg246Arg=) TSC1 not provided 9:135787844
TTN:c.50355A>G (p.Arg16785=) TTN Uncertain significance 2:179476681
USH2A:c.6486G>A (p.Gln2162=) USH2A Likely benign 1:216172400
ZNF335:c.2703C>T (p.Ser901=) ZNF335 Benign 20:44581348
E1_A_PLUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
AATF:c.1620G>A (p.Arg540Arg=) AATF not provided 17:35413901
ATP2C1:c.2127G>A (p.Thr709Thr=) ATP2C1 not provided 3:130715524
ATP6V0A2:c.1515T>C (p.Asn505=) ATP6V0A2 Benign 12:124229429
B3GALTL:c.348T>C (p.His116His=) B3GALTL Benign 13:31821992
CHD7:c.4851T>C (p.Gly1617=) CHD7 Uncertain significance 8:61757423
DSP:c.2631G>A (p.Arg877=) DSP Benign 6:7576527
GALNT13:c.687G>A (p.Arg229Arg=) GALNT13 not provided 2:155102325
ITPR1:c.1962G>A (p.Lys654=) ITPR1 Benign 3:4712413
KIF1B:c.4809G>A (p.Lys1603Lys=) KIF1B not provided 1:10434374
LGR6:c.999G>A (p.Leu333Leu=) LGR6 not provided 1:202273687
LMNA:c.357C>T (p.Arg119Arg=) LMNA Benign;Uncertain significance 1:156100408
LMO7:c.3186G>A (p.Arg1062Arg=) LMO7 not provided 13:76416987
MYO7A:c.2283G>A (p.Arg761Arg=) MYO7A Likely benign 11:76890091
NPSR1:c.1026G>A (p.Arg342Arg=) NPSR1 not provided 7:34889177
NRG3:c.1158G>A (p.Lys386Lys=) NRG3 not provided 10:84718705
OSBPL2:c.456G>A (p.Arg152Arg=) OSBPL2 not provided 20:60854213
PIWIL4:c.1269G>A (p.Arg423Arg=) PIWIL4 not provided 11:94330970
PLCB1:c.3337C>T (p.Leu1113=) PLCB1 Benign 20:8770822
RUNDC3B:c.459G>A (p.Arg153Arg=) RUNDC3B not provided 7:87369107
SLC4A10:c.1443G>A (p.Arg481Arg=) SLC4A10 not provided 2:162760514
STXBP1:c.1548C>T (p.Ser516=) STXBP1 Uncertain significance 9:130444685
TRPM2:c.255G>A (p.Gly85Gly=) TRPM2 not provided 21:45783997
Ez_D_MINUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
ABCA4:c.768G>T (p.Val256=) ABCA4 not provided 1:94564350
AKT2:c.960G>A (p.Glu320=) AKT2 Uncertain significance 19:40742164
BRCA1:c.4185G>A (p.Gln1395Gln=) BRCA1 Pathogenic 17:41242961
BRCA1:c.5277G>A (p.Lys1759Lys=) BRCA1 Pathogenic 17:41209069
CA5A:c.555G>A (p.Lys185=) CA5A Pathogenic 16:87936031
CORO1C:c.195G>A (p.Lys65Lys=) CORO1C not provided 12:109094900
CPAMD8:c.627G>A (p.Lys209Lys=) CPAMD8 not provided 19:17122274
CSTB:c.168G>A (p.Lys56=) CSTB Likely pathogenic 21:45194539
CSTB:c.66G>A (p.Gln22=) CSTB Likely pathogenic 21:45196085
CUBN:c.1530G>A (p.Lys510=) CUBN Likely pathogenic 10:17145124
CUBN:c.489G>A (p.Lys163=) CUBN Likely pathogenic 10:17165587
DPYD:c.1905C>T (p.Asn635Asn=) DPYD not provided 1:97915615
GAMT:c.327G>A (p.Lys109Lys=) GAMT Pathogenic 19:1399792
GCK:c.483G>A (p.Lys161Lys=) GCK Likely pathogenic 7:44190555
GNPTAB:c.771G>A (p.Leu257Leu=) GNPTAB Pathogenic 12:102173930
KMT2D:c.10740G>A (p.Gln3580=) KMT2D Likely pathogenic 12:49427850
LAMA4:c.3813G>A (p.Gly1271=) LAMA4 Uncertain significance 6:112453955
MKS1:c.387G>A (p.Glu129=) MKS1 Likely pathogenic 17:56293449
MLC1:c.597A>G (p.Ser199=) MLC1 Benign 22:50515270
MYH7:c.2922G>A (p.Lys974=) MYH7 Likely benign 14:23893116

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Email:mehisp@hotmail.com
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MYH7:c.345C>T (p.Tyr115=) MYH7 Uncertain significance 14:23902293
MYH7:c.732C>T (p.Phe244=) MYH7 Benign 14:23900794
NEB:c.18693G>C (p.Ala6231=) NEB Benign 2:152420120
NEB:c.2943G>A (p.Glu981=) NEB Uncertain significance 2:152539176
NPHS2:c.378G>A (p.Lys126Lys=) NPHS2 not provided 1:179533825
PAH:c.168G>A (p.Glu56=) PAH not provided 12:103306569
PAH:c.912G>A (p.Gln304=) PAH not provided 12:103245465
PAH:c.969A>G (p.Thr323=) PAH not provided 12:103240673
PRKAG2:c.114G>A (p.Pro38=) PRKAG2 Likely benign 7:151573592
PYGM:c.1827G>A (p.Lys609Lys=) PYGM Pathogenic 11:64519069
RBM19:c.2385G>A (p.Gln795=) RBM19 Uncertain significance 12:114358416
RRM2B:c.48G>A (p.Glu16=) RRM2B Pathogenic 8:103251055
SLC17A5:c.291G>A (p.Thr97=) SLC17A5 Likely pathogenic 6:74354130
SLC25A13:c.15G>A (p.Lys5Lys=) SLC25A13 Pathogenic 7:95951254
TBC1D4:c.1611T>G (p.Ser537=) TBC1D4 Benign 13:75915261
TP53:c.672G>A (p.Glu224Glu=) TP53 not provided 17:7578177
TSC1:c.363G>A (p.Lys121Lys=) TSC1 not provided 9:135800974
VWF:c.7437G>A (p.Ser2479=) VWF not provided 12:6085277
WDR74:c.618G>A (p.Gln206Gln=) - not provided 11:62602903
Ez_D_PLUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
ATM:c.2250G>A (p.Lys750=) ATM Likely pathogenic;Pathogenic 11:108127067
ATM:c.3576G>A (p.Lys1192=) ATM Pathogenic 11:108151895
ATP8A2:c.2679G>A (p.Glu893Glu=) ATP8A2 not provided 13:26349097
ATP8B2:c.3393G>A (p.Thr1131Thr=) ATP8B2 not provided 1:154321014
BCKDHA:c.288C>T (p.His96=) BCKDHA Uncertain significance 19:41916721
BRCA2:c.516G>A (p.Lys172Lys=) BRCA2 Uncertain significance 13:32900419
BRCA2:c.8331G>A (p.Lys2777Lys=) BRCA2 Uncertain significance 13:32937670
BRCA2:c.8754G>A (p.Glu2918Glu=) BRCA2 Pathogenic 13:32950928
BRCA2:c.9117G>A (p.Pro3039Pro=) BRCA2 Pathogenic 13:32954050
BRCA2:c.9501G>A (p.Glu3167Glu=) BRCA2 Pathogenic 13:32969070
BTD:c.459G>A (p.Glu153Glu=) BTD Pathogenic 3:15683564
CCDC83:c.672G>A (p.Glu224Glu=) CCDC83 not provided 11:85610058
CCND1:c.723G>A (p.Pro241=) CCND1 risk factor 11:69462910
CD22:c.1944G>A (p.Lys648Lys=) CD22 not provided 19:35836029
CD96:c.855G>A (p.Glu285Glu=) CD96 not provided 3:111304225
CDH23:c.7362G>A (p.Thr2454=) CDH23 Likely pathogenic 10:73559386
CFTR:c.1209G>A (p.Glu403=) CFTR not provided 7:117182162
CFTR:c.1584G>A (p.Glu528=) CFTR Benign;Uncertain significance 7:117199709
CFTR:c.2619G>A (p.Glu873=) CFTR not provided 7:117235112
CFTR:c.2988G>A (p.Gln996Gln=) CFTR
Pathogenic;Uncertain
significance 7:117246807
CFTR:c.3468G>A (p.Leu1156=) CFTR not provided 7:117254767
CFTR:c.3717G>A (p.Arg1239=) CFTR not provided 7:117267824
CFTR:c.489G>A (p.Lys163=) CFTR not provided 7:117171168
CHRND:c.243C>T (p.His81=) CHRND Benign 2:233392155
CNTNAP2:c.1083G>A (p.Val361=) CNTNAP2 Benign;Uncertain significance 7:146825928
COL3A1:c.2022G>A (p.Lys674=) COL3A1 Pathogenic 2:189863444
COL3A1:c.2337G>A (p.Lys779=) COL3A1 Pathogenic 2:189866176
COL3A1:c.4254G>A (p.Thr1418=) COL3A1 Pathogenic 2:189875616
COL6A1:c.1056C>T (p.Asp352=) COL6A1 Benign 21:47410740
CYP27A1:c.1017G>C (p.Thr339=) CYP27A1 Pathogenic 2:219677819
DYSF:c.6009G>A (p.Ala2003=) DYSF Uncertain significance 2:71906365
EGFLAM:c.2166G>A (p.Glu722Glu=) EGFLAM not provided 5:38431390
ERGIC1:c.765G>A (p.Thr255Thr=) ERGIC1 not provided 5:172362313
FBXW12:c.33G>A (p.Lys11Lys=) FBXW12 not provided 3:48413810
FRMPD1:c.612G>A (p.Lys204Lys=) FRMPD1 not provided 9:37724317
GRN:c.264G>A (p.Glu88=) GRN not provided 17:42426919
GRN:c.708C>T (p.Asn236=) GRN not provided 17:42428168

5. Mehis Pold, MD
Email:mehisp@hotmail.com
5
HAS3:c.636G>A (p.Gln212Gln=) HAS3 not provided 16:69143934
KCNQ1:c.1032G>A (p.Ala344Ala=) KCNQ1 Pathogenic 11:2604775
KCNQ1:c.1032G>C (p.Ala344=) KCNQ1 not provided 11:2604775
KCNQ1:c.921G>A (p.Val307=) KCNQ1 not provided 11:2594216
LMNA:c.1698C>T (p.His566His=) LMNA Benign 1:156107534
LMNA:c.513G>A (p.Lys171Lys=) LMNA not provided 1:156100564
LMNA:c.810G>A (p.Lys270Lys=) LMNA not provided 1:156104766
MAPT:c.1866T>C (p.Ser622=) MAPT not provided 17:44087768
MLH1:c.1038G>A (p.Gln346Gln=) MLH1 Pathogenic 3:37061954
MLH1:c.1731G>A (p.Ser577Ser=) MLH1 Pathogenic 3:37083822
MLH1:c.1731G>C (p.Ser577=) MLH1 Uncertain significance 3:37083822
MLH1:c.1896G>A (p.Glu632Glu=) MLH1 Pathogenic 3:37089174
MLH1:c.1989G>A (p.Glu663Glu=) MLH1 Likely pathogenic 3:37090100
MLH1:c.2103G>A (p.Gln701=) MLH1 Likely pathogenic 3:37090508
MLH1:c.453G>A (p.Thr151=) MLH1 Likely pathogenic 3:37048554
MSH2:c.2634G>A (p.Glu878=) MSH2 Pathogenic 2:47708010
MSH2:c.942G>A (p.Gln314=) MSH2 Pathogenic 2:47641557
MYH14:c.810C>T (p.Phe270=) MYH14 Likely benign 19:50728934
MYOCD:c.1125G>A (p.Lys375Lys=) MYOCD not provided 17:12649389
NISCH:c.1653G>A (p.Gln551Gln=) NISCH not provided 3:52518653
PNLDC1:c.1224C>T (p.Ile408Ile=) PNLDC1 not provided 6:160239686
PRRG2:c.261G>A (p.Thr87Thr=) - not provided 19:50086974
SERPING1:c.51G>A (p.Gly17Gly=) SERPING1 not provided 11:57365794
SLC26A4:c.1614C>T (p.Asn538Asn=) SLC26A4 Likely benign 7:107338556
SLC26A4:c.918G>A (p.Val306Val=) SLC26A4 not provided 7:107323799
SLC34A3:c.756G>A (p.Gln252Gln=) SLC34A3 Pathogenic 9:140127856
SLC34A3:c.846G>A (p.Pro282Pro=) SLC34A3 Pathogenic 9:140128174
TGFBR2:c.1524G>A (p.Gln508Gln=) TGFBR2 Pathogenic 3:30730003
TSC2:c.1443G>A (p.Glu481Glu=) TSC2 not provided 16:2113054
TSC2:c.1599G>A (p.Lys533Lys=) TSC2 not provided 16:2114428
TSC2:c.1716G>A (p.Gln572=) TSC2 not provided 16:2115636
TSC2:c.2742G>A (p.Lys914Lys=) TSC2 not provided 16:2126171
TSC2:c.4662G>A (p.Gln1554Gln=) TSC2 not provided 16:2135323
TTC8:c.489G>A (p.Thr163Thr=) TTC8 Pathogenic 14:89307540
UROD:c.942G>A (p.Glu314Glu=) UROD Pathogenic 1:45480678
VPS13B:c.1563G>A (p.Lys521Lys=) VPS13B Pathogenic 8:100147961
I1_D_MINUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
KCNQ2:c.1119G>A (p.Arg373Arg=) KCNQ2 Pathogenic 20:62065161
PAX3:c.1449G>A (p.Ala483Ala=) PAX3 not provided 2:223066130
PTHLH:c.525G>A (p.Arg175Arg=) PTHLH not provided 12:28116280
I2_D_MINUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
BRCA1:c.789T>C (p.Gly263=) BRCA1 not provided 17:41246759
I2_D_PLUS
Variant Description Gene ID Pathogenicity
Genome
Coordinates
EPGN:c.108T>C (p.Gly36=) EPGN not provided 4:75174874
MLH1:c.303T>G (p.Gly101Gly=) MLH1 Likely benign 3:37042541