ClinVar Miner

Variants with conflicting interpretations between Genome Diagnostics Laboratory, Amsterdam University Medical Center and Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Minimum review status of the submission from Genome Diagnostics Laboratory, Amsterdam University Medical Center: Collection method of the submission from Genome Diagnostics Laboratory, Amsterdam University Medical Center:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic) 		Variants with a confidence conflict
(e.g. benign vs likely benign) 		Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects) 		Variants with a clinically significant conflict
(e.g. benign vs pathogenic) 		Variants with any conflict
114 802 0 159 0 0 0 159

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

pathogenic likely pathogenic likely benign benign
pathogenic 0 22 0 0
likely pathogenic 22 0 0 0
likely benign 0 0 0 33
benign 0 0 82 0

All variants with conflicting interpretations #

Total variants: 159
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_014694.4(ADAMTSL2):c.2313A>G (p.Val771=) rs1064975 0.61566
NM_014694.4(ADAMTSL2):c.1641C>T (p.His547=) rs7868941 0.16167
NM_001734.5(C1S):c.356G>A (p.Arg119His) rs12146727 0.12113
NM_002335.4(LRP5):c.3989C>T (p.Ala1330Val) rs3736228 0.10701
NM_024306.5(FA2H):c.1039+16T>G rs7193407 0.07963
NM_144997.7(FLCN):c.1233G>A (p.Glu411=) rs61750032 0.03557
NM_004360.5(CDH1):c.48+5C>G rs77312180 0.03370
NM_002474.3(MYH11):c.5370C>T (p.Leu1790=) rs35295469 0.03116
NM_002693.3(POLG):c.3428A>G (p.Glu1143Gly) rs2307441 0.02704
NM_000455.5(STK11):c.816C>T (p.Tyr272=) rs9282859 0.02603
NM_000142.5(FGFR3):c.615+8C>G rs17878375 0.02283
NM_000096.4(CP):c.1652C>T (p.Thr551Ile) rs61733458 0.02154
NM_004260.4(RECQL4):c.3393+9A>G rs4251692 0.02095
NM_000142.5(FGFR3):c.1076-17C>T rs17881967 0.02051
NM_000142.5(FGFR3):c.1075+5C>T rs3135885 0.01659
NM_017617.5(NOTCH1):c.3836G>A (p.Arg1279His) rs61751543 0.01655
NM_152296.5(ATP1A3):c.994-20T>G rs138485069 0.01603
NM_024675.4(PALB2):c.1010T>C (p.Leu337Ser) rs45494092 0.01508
NM_001370259.2(MEN1):c.512G>A (p.Arg171Gln) rs607969 0.01309
NM_025137.4(SPG11):c.1348A>G (p.Ile450Val) rs3759873 0.01282
NM_000096.4(CP):c.2378G>A (p.Arg793His) rs115552500 0.01239
NM_017617.5(NOTCH1):c.2691C>T (p.Ala897=) rs11574895 0.01135
NM_000096.4(CP):c.2286-12T>G rs183671127 0.01016
NM_001048174.2(MUTYH):c.1460C>T (p.Ser487Phe) rs140118273 0.00997
NM_000141.5(FGFR2):c.294G>A (p.Thr98=) rs1047101 0.00776
NM_152296.5(ATP1A3):c.2487G>A (p.Pro829=) rs45606534 0.00759
NM_017617.5(NOTCH1):c.3780G>C (p.Val1260=) rs201354526 0.00754
NM_003002.4(SDHD):c.149A>G (p.His50Arg) rs11214077 0.00679
NM_000038.6(APC):c.5265G>A (p.Ala1755=) rs34506289 0.00675
NM_000791.4(DHFR):c.-259C>T rs6151597 0.00658
NM_005633.4(SOS1):c.1074+5G>C rs145155424 0.00655
NM_000455.5(STK11):c.369G>A (p.Gln123=) rs140112347 0.00636
NM_000071.3(CBS):c.1145+7C>T rs201158177 0.00620
NM_000051.4(ATM):c.5793T>C (p.Ala1931=) rs3092910 0.00608
NM_001048174.2(MUTYH):c.1347G>C (p.Thr449=) rs74318065 0.00596
NM_000038.6(APC):c.1959G>A (p.Arg653=) rs72541809 0.00583
NM_000138.5(FBN1):c.5343G>A (p.Val1781=) rs140649 0.00561
NM_017617.5(NOTCH1):c.5124G>T (p.Ser1708=) rs35980907 0.00561
NM_006767.4(LZTR1):c.1209C>T (p.Phe403=) rs145833752 0.00550
NM_058216.3(RAD51C):c.572-17G>T rs193023469 0.00513
NM_000142.5(FGFR3):c.663G>A (p.Ser221=) rs114421370 0.00485
NM_024675.4(PALB2):c.2794G>A (p.Val932Met) rs45624036 0.00449
NM_001110556.2(FLNA):c.1176G>A (p.Glu392=) rs201173693 0.00446
NM_000138.5(FBN1):c.6594C>T (p.Pro2198=) rs111844882 0.00439
NM_000138.5(FBN1):c.1746C>T (p.Cys582=) rs112366266 0.00436
NM_000138.5(FBN1):c.4905C>G (p.Thr1635=) rs113115949 0.00435
NM_004656.4(BAP1):c.2057-4G>T rs149499021 0.00433
NM_004168.4(SDHA):c.969C>T (p.Gly323=) rs142849100 0.00430
NM_004360.5(CDH1):c.532-18C>T rs200673941 0.00398
NM_017617.5(NOTCH1):c.4536C>T (p.Ala1512=) rs61751540 0.00377
NM_004656.4(BAP1):c.1729+8T>C rs150945583 0.00364
NM_000051.4(ATM):c.5497-15G>C rs3092828 0.00363
NM_000548.5(TSC2):c.2031C>T (p.Pro677=) rs45517208 0.00361
NM_000275.3(OCA2):c.1327G>A (p.Val443Ile) rs121918166 0.00350
NM_058216.3(RAD51C):c.376G>A (p.Ala126Thr) rs61758784 0.00349
NM_017617.5(NOTCH1):c.2207+10G>A rs191892426 0.00343
NM_000245.4(MET):c.2908C>T (p.Arg970Cys) rs34589476 0.00327
NM_000501.4(ELN):c.2132G>A (p.Gly711Asp) rs41511151 0.00318
NM_017617.5(NOTCH1):c.2542G>A (p.Glu848Lys) rs35136134 0.00318
NM_004656.4(BAP1):c.1002A>G (p.Leu334=) rs28997577 0.00310
NM_000038.6(APC):c.3471G>A (p.Glu1157=) rs143927847 0.00308
NM_003238.6(TGFB2):c.272G>A (p.Arg91His) rs10482721 0.00297
NM_000038.6(APC):c.3165A>T (p.Ile1055=) rs61734287 0.00286
NM_017617.5(NOTCH1):c.3294C>T (p.Ser1098=) rs61751546 0.00283
NM_000057.4(BLM):c.1928G>A (p.Arg643His) rs12720097 0.00278
NM_001844.5(COL2A1):c.2334C>T (p.Ala778=) rs35504014 0.00278
NM_000136.3(FANCC):c.584A>T (p.Asp195Val) rs1800365 0.00275
NM_005359.6(SMAD4):c.354G>A (p.Ala118=) rs145988618 0.00268
NM_000551.4(VHL):c.74C>T (p.Pro25Leu) rs35460768 0.00261
NM_004360.5(CDH1):c.1680G>C (p.Thr560=) rs35741240 0.00261
NM_004360.5(CDH1):c.324A>G (p.Arg108=) rs116542018 0.00255
NM_198253.3(TERT):c.1812A>G (p.Ala604=) rs33959226 0.00255
NM_002335.4(LRP5):c.4431C>T (p.His1477=) rs11574426 0.00238
NM_005359.6(SMAD4):c.1086T>C (p.Phe362=) rs1801250 0.00228
NM_017617.5(NOTCH1):c.2734C>T (p.Arg912Trp) rs201620358 0.00223
NM_000094.4(COL7A1):c.5988C>T (p.Ile1996=) rs146901730 0.00220
NM_002474.3(MYH11):c.3652-6C>T rs193922630 0.00219
NM_000094.4(COL7A1):c.5910C>T (p.Phe1970=) rs141290741 0.00212
NM_024675.4(PALB2):c.721A>G (p.Asn241Asp) rs113217267 0.00202
NM_007194.4(CHEK2):c.254C>T (p.Pro85Leu) rs17883862 0.00201
NM_001113378.2(FANCI):c.3592-8T>C rs185599057 0.00200
NM_004168.4(SDHA):c.1551+16C>T rs184954254 0.00198
NM_024675.4(PALB2):c.1606C>T (p.Leu536=) rs151162255 0.00193
NM_024675.4(PALB2):c.2256A>G (p.Gly752=) rs147120218 0.00193
NM_004168.4(SDHA):c.1911C>T (p.Val637=) rs11557098 0.00180
NM_017617.5(NOTCH1):c.3315G>T (p.Ala1105=) rs3812602 0.00175
NM_002693.3(POLG):c.1760C>T (p.Pro587Leu) rs113994096 0.00160
NM_006361.6(HOXB13):c.251G>A (p.Gly84Glu) rs138213197 0.00160
NM_003000.3(SDHB):c.300T>C (p.Ser100=) rs11541235 0.00157
NM_001042492.3(NF1):c.846G>A (p.Gln282=) rs138840528 0.00149
NM_004004.6(GJB2):c.380G>A (p.Arg127His) rs111033196 0.00143
NM_152296.5(ATP1A3):c.816G>A (p.Thr272=) rs149898088 0.00140
NM_177438.3(DICER1):c.5145C>T (p.Leu1715=) rs139500905 0.00121
NM_017617.5(NOTCH1):c.2970-20G>A rs367927174 0.00116
NM_032043.3(BRIP1):c.890A>G (p.Lys297Arg) rs28997570 0.00113
NM_024675.4(PALB2):c.1194G>A (p.Val398=) rs61755173 0.00103
NM_024675.4(PALB2):c.909C>T (p.Leu303=) rs145788619 0.00101
NM_001854.4(COL11A1):c.1021G>C (p.Glu341Gln) rs144884147 0.00098
NM_000142.5(FGFR3):c.1349C>T (p.Thr450Met) rs56240927 0.00083
NM_002474.3(MYH11):c.3102T>C (p.Ser1034=) rs181744522 0.00080
NM_003754.3(EIF3F):c.694T>G (p.Phe232Val) rs141976414 0.00080
NM_000455.5(STK11):c.*16+10G>A rs587781180 0.00077
NM_000535.7(PMS2):c.2187C>G (p.Leu729=) rs373630535 0.00077
NM_005188.4(CBL):c.2269G>A (p.Ala757Thr) rs146517083 0.00076
NM_000051.4(ATM):c.1744T>C (p.Phe582Leu) rs2235006 0.00071
NM_000179.3(MSH6):c.1526T>C (p.Val509Ala) rs63751005 0.00067
NM_000393.5(COL5A2):c.3837T>C (p.Ile1279=) rs148795690 0.00065
NM_030777.4(SLC2A10):c.765C>T (p.Ser255=) rs142106322 0.00065
NM_017617.5(NOTCH1):c.4917C>T (p.Ala1639=) rs371365065 0.00058
NM_000455.5(STK11):c.1211C>T (p.Ser404Phe) rs200078204 0.00051
NM_138694.4(PKHD1):c.107C>T (p.Thr36Met) rs137852944 0.00048
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_017807.4(OSGEP):c.328T>C (p.Cys110Arg) rs140076803 0.00036
NM_000051.4(ATM):c.6919C>T (p.Leu2307Phe) rs56009889 0.00035
NM_000492.4(CFTR):c.3454G>C (p.Asp1152His) rs75541969 0.00033
NM_000546.6(TP53):c.704A>G (p.Asn235Ser) rs144340710 0.00025
NM_000414.4(HSD17B4):c.46G>A (p.Gly16Ser) rs137853096 0.00019
NM_001282225.2(ADA2):c.973-2A>G rs139750129 0.00018
NM_000135.4(FANCA):c.2852G>A (p.Arg951Gln) rs755922289 0.00013
NM_014780.5(CUL7):c.3041T>G (p.Leu1014Arg) rs61752334 0.00011
NM_024753.5(TTC21B):c.626C>T (p.Pro209Leu) rs140511594 0.00011
NM_001358530.2(MOCS1):c.418+1G>A rs141982812 0.00006
NM_020533.3(MCOLN1):c.1084G>T (p.Asp362Tyr) rs121908372 0.00004
NM_000079.4(CHRNA1):c.317G>A (p.Trp106Ter) rs1476453955 0.00003
NM_000492.4(CFTR):c.1040G>A (p.Arg347His) rs77932196 0.00003
NM_000051.4(ATM):c.8730C>G (p.Leu2910=) rs551041839 0.00001
NM_000083.3(CLCN1):c.1471+1G>A rs375596425 0.00001
NM_000089.4(COL1A2):c.838G>A (p.Gly280Ser) rs72656387 0.00001
NM_000263.4(NAGLU):c.1927C>T (p.Arg643Cys) rs104894594 0.00001
NM_000834.5(GRIN2B):c.1555C>T (p.Arg519Ter) rs774592932 0.00001
NM_001164508.2(NEB):c.22831C>T (p.Arg7611Ter) rs555582398 0.00001
NM_004168.4(SDHA):c.1753C>T (p.Arg585Trp) rs200397144 0.00001
NM_017807.4(OSGEP):c.332T>C (p.Ile111Thr) rs1443735811 0.00001
NM_138422.4(ADAT3):c.430G>A (p.Val144Met) rs730882213 0.00001
NM_178452.6(DNAAF1):c.1528+2T>C rs569633512 0.00001
NM_000092.5(COL4A4):c.3289+1G>T rs1973128133
NM_000264.5(PTCH1):c.1602+15_1602+17del rs528001004
NM_000282.4(PCCA):c.1409T>G (p.Leu470Arg) rs2152697481
NM_000314.8(PTEN):c.103A>G (p.Met35Val) rs876659443
NM_000466.3(PEX1):c.2097dup (p.Ile700fs) rs61750415
NM_000478.6(ALPL):c.472+12del rs35423948
NM_000501.4(ELN):c.1741G>C (p.Gly581Arg) rs17855988
NM_001127222.2(CACNA1A):c.4979G>A (p.Arg1660His) rs121908216
NM_001134232.2(TMEM106B):c.754G>A (p.Asp252Asn) rs1554310600
NM_001253852.3(AP4B1):c.616C>T (p.Arg206Ter) rs762612591
NM_001256715.2(DNAAF3):c.1271dup (p.Phe426fs) rs1349668884
NM_001354604.2(MITF):c.1096C>T (p.Arg366Ter) rs2066482593
NM_001356.5(DDX3X):c.1807C>T (p.Arg603Ter) rs886041705
NM_001958.5(EEF1A2):c.271G>A (p.Asp91Asn) rs886041197
NM_002087.4(GRN):c.1252C>T (p.Arg418Ter) rs63751180
NM_002335.4(LRP5):c.1828G>A (p.Gly610Arg) rs80358313
NM_005032.7(PLS3):c.1262+1G>A rs868979288
NM_006516.4(SLC2A1):c.940G>A (p.Gly314Ser) rs121909739
NM_012062.5(DNM1L):c.1207C>T (p.Arg403Cys) rs863223953
NM_015046.7(SETX):c.4630_4631del (p.Leu1544fs) rs1356107030
NM_018684.4(ZC4H2):c.592C>T (p.Arg198Trp) rs137962226
NM_152296.5(ATP1A3):c.1323G>A (p.Ala441=) rs34578730
NM_177559.3(CSNK2A1):c.149A>G (p.Tyr50Cys) rs869312849
NM_198578.4(LRRK2):c.4193G>A (p.Arg1398His) rs7133914

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