ClinVar Miner

List of variants reported as benign for central nervous system malformation by Genome-Nilou Lab

Included ClinVar conditions (163):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 211
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001384732.1(CPLANE1):c.81+20= rs6876576 0.99994
NM_004958.4(MTOR):c.6034-30A>G rs1770344 0.99413
NM_021926.4(ALX4):c.621A>G (p.Ser207=) rs10769028 0.99242
NM_001759.4(CCND2):c.-49T>C rs3217786 0.97216
NM_001128159.3(VPS53):c.1117-26T>C rs4968055 0.96284
NM_021926.4(ALX4):c.467-45T>C rs11037929 0.95917
NM_005027.4(PIK3R2):c.937T>C (p.Ser313Pro) rs1011320 0.95640
NM_001378615.1(CC2D2A):c.4065+28A>T rs6832789 0.95451
NM_005027.4(PIK3R2):c.700A>C (p.Ser234Arg) rs2241088 0.93443
NM_025114.4(CEP290):c.6645+67G>A rs2471512 0.92687
NM_000435.3(NOTCH3):c.4563A>G (p.Pro1521=) rs1044006 0.90693
NM_000435.3(NOTCH3):c.5913+28T>G rs4809029 0.90682
NM_000435.3(NOTCH3):c.5362+3T>C rs1548555 0.90675
NM_000435.3(NOTCH3):c.5816-8T>C rs4809030 0.90632
NM_000435.3(NOTCH3):c.5815+36G>A rs2074618 0.90515
NM_000435.3(NOTCH3):c.5363-21G>A rs10416777 0.90510
NM_000435.3(NOTCH3):c.5363-17C>T rs2074619 0.90508
NM_207346.3(TSEN54):c.1122G>C (p.Arg374=) rs6501820 0.89534
NM_025114.4(CEP290):c.853-12_853-11insG rs71082425 0.87640
NM_000435.3(NOTCH3):c.1192+15A>G rs10423702 0.87325
NM_000435.3(NOTCH3):c.606A>G (p.Ala202=) rs1043994 0.87319
NM_000435.3(NOTCH3):c.5913+55A>G rs757472 0.86388
NM_005027.4(PIK3R2):c.1911T>C (p.Ser637=) rs273269 0.85598
NM_001378615.1(CC2D2A):c.247+26A>G rs10000250 0.85216
NM_001173990.3(TMEM216):c.264G>A (p.Pro88=) rs3741265 0.84043
NM_005559.4(LAMA1):c.5380-13G>A rs617573 0.82747
NM_005559.4(LAMA1):c.5496+20A>G rs616722 0.82650
NM_001134831.2(AHI1):c.1780-14C>T rs2757645 0.81825
NM_015272.5(RPGRIP1L):c.1104-82C>T rs4133017 0.80982
NM_014875.3(KIF14):c.3096A>G (p.Glu1032=) rs6665951 0.79936
NM_021926.4(ALX4):c.778-117T>C rs10742699 0.79676
NM_002449.5(MSX2):c.386T>C (p.Met129Thr) rs4242182 0.78320
NM_000435.3(NOTCH3):c.2742A>G (p.Pro914=) rs1043997 0.76937
NM_025114.4(CEP290):c.2818-50G>C rs2471532 0.76931
NM_000435.3(NOTCH3):c.2792+21G>A rs11669982 0.76928
NM_001378615.1(CC2D2A):c.1764+45T>G rs1558572 0.75139
NM_001368809.2(AMPD2):c.860+19A>G rs524998 0.73896
NM_001134831.2(AHI1):c.10+115C>A rs9402709 0.73311
NM_033026.6(PCLO):c.2441G>C (p.Ser814Thr) rs2877 0.70660
NM_001368809.2(AMPD2):c.1272T>C (p.His424=) rs863978 0.70414
NM_001378615.1(CC2D2A):c.3183-8T>C rs13121363 0.69106
NM_000435.3(NOTCH3):c.6668C>T (p.Ala2223Val) rs1044009 0.69087
NM_001378615.1(CC2D2A):c.3595-55C>G rs4280723 0.69017
NM_001378615.1(CC2D2A):c.3288+41A>C rs13116304 0.68417
NM_005559.4(LAMA1):c.6004A>G (p.Lys2002Glu) rs607230 0.68054
NM_001044385.3(TMEM237):c.274+23A>G rs1208081 0.64988
NM_207346.3(TSEN54):c.285+32C>A rs7218675 0.64612
NM_000435.3(NOTCH3):c.3461-32C>T rs56061231 0.63976
NM_207346.3(TSEN54):c.1310C>T (p.Ala437Val) rs8064529 0.63819
NM_033026.6(PCLO):c.1893+47C>A rs6951239 0.63627
NM_004958.4(MTOR):c.2997C>T (p.Asn999=) rs1064261 0.63488
NM_001128159.3(VPS53):c.2328+15A>G rs2034088 0.63097
NM_020320.5(RARS2):c.1512-43T>C rs9450723 0.61345
NM_020320.5(RARS2):c.452-21A>G rs4707374 0.61261
NM_005559.4(LAMA1):c.2763T>C (p.Cys921=) rs539713 0.61217
NM_016111.4(TELO2):c.682+115C>T rs2235630 0.61186
NM_001082486.2(ACD):c.1295T>C (p.Val432Ala) rs6979 0.60624
NM_207346.3(TSEN54):c.12G>T (p.Glu4Asp) rs7216673 0.60248
NM_000435.3(NOTCH3):c.4892-22G>T rs2074620 0.59905
NM_004958.4(MTOR):c.1437T>C (p.Asp479=) rs1135172 0.59749
NM_001134831.2(AHI1):c.3426+13G>A rs6914831 0.59084
NM_207346.3(TSEN54):c.1041G>C (p.Lys347Asn) rs9911502 0.58492
NM_020335.3(VANGL2):c.1137A>G (p.Lys379=) rs12086448 0.58424
NM_021926.4(ALX4):c.778-140G>C rs10769024 0.57195
NM_001378615.1(CC2D2A):c.*21G>C rs1134634 0.57021
NM_000435.3(NOTCH3):c.3837+21T>A rs11670823 0.56639
NM_000435.3(NOTCH3):c.2538C>T (p.Cys846=) rs1043996 0.56438
NM_004958.4(MTOR):c.4731G>A (p.Ala1577=) rs1057079 0.55171
NM_016042.4(EXOSC3):c.498G>A (p.Gln166=) rs7158 0.53959
NM_017777.4(MKS1):c.858+9A>G rs3826300 0.53797
NM_017777.4(MKS1):c.750-105T>C rs3744105 0.53777
NM_014875.3(KIF14):c.4020G>A (p.Glu1340=) rs7543730 0.53314
NM_001378615.1(CC2D2A):c.1765-24A>G rs1861044 0.52969
NM_178161.3(PTF1A):c.787T>C (p.Ser263Pro) rs7918487 0.51842
NM_001128159.3(VPS53):c.1557-30T>C rs741677 0.51785
NM_016111.4(TELO2):c.437A>G (p.Gln146Arg) rs2235624 0.51194
NM_001199198.3(TBC1D23):c.876+27G>T rs3772698 0.50657
NM_014008.5(CCDC22):c.1540-18T>C rs2294021 0.50585
NM_025233.7(COASY):c.164C>A (p.Ser55Tyr) rs615942 0.49854
NM_025233.7(COASY):c.972A>G (p.Thr324=) rs598126 0.49440
NM_005559.4(LAMA1):c.3378T>C (p.Gly1126=) rs9946794 0.48883
NM_005559.4(LAMA1):c.2493T>C (p.Cys831=) rs684634 0.48817
NM_005559.4(LAMA1):c.5391G>A (p.Leu1797=) rs617206 0.48492
NM_005559.4(LAMA1):c.5496+19C>T rs523711 0.48483
NM_001128159.3(VPS53):c.1218+817A>G rs11247553 0.48461
NM_005559.4(LAMA1):c.2109C>T (p.Ala703=) rs621993 0.46872
NM_005559.4(LAMA1):c.2051+14A>T rs674733 0.46819
NM_033026.6(PCLO):c.14415+10T>C rs2715150 0.44882
NM_001128159.3(VPS53):c.-90C>T rs2474694 0.44823
NM_021926.4(ALX4):c.104G>C (p.Arg35Thr) rs3824915 0.42227
NM_016111.4(TELO2):c.2226+38A>G rs11248882 0.42009
NM_018027.5(FRMD4A):c.207-16T>C rs3740121 0.41756
NM_016111.4(TELO2):c.2021A>G (p.Gln674Arg) rs2248128 0.41062
NM_001128159.3(VPS53):c.1867-81C>T rs7219151 0.40515
NM_015272.5(RPGRIP1L):c.2959-32G>A rs7203525 0.39281
NM_005559.4(LAMA1):c.3573C>T (p.Thr1191=) rs619106 0.39038
NM_018718.3(CEP41):c.-5A>C rs2287371 0.39010
NM_001128159.3(VPS53):c.218+102C>G rs2543781 0.38294
NM_001128178.3(NPHP1):c.654G>A (p.Glu218=) rs11675767 0.38033
NM_033026.6(PCLO):c.1501T>C (p.Ser501Pro) rs6972461 0.37994
NM_015272.5(RPGRIP1L):c.*55T>A rs4784319 0.37955
NM_016111.4(TELO2):c.2415T>C (p.Ala805=) rs3180228 0.37206
NM_001497.4(B4GALT1):c.648+102C>T rs913214 0.35792
NM_017777.4(MKS1):c.261+67A>G rs7225148 0.34782
NM_003384.3(VRK1):c.217-244T>C rs12586511 0.34167
NM_001128159.3(VPS53):c.1524C>T (p.Tyr508=) rs2075443 0.33961
NM_033026.6(PCLO):c.14440T>G (p.Ser4814Ala) rs2522833 0.33644
NM_021926.4(ALX4):c.304C>T (p.Pro102Ser) rs12421995 0.32933
NM_003384.3(VRK1):c.705C>T (p.Gly235=) rs2230532 0.32707
NM_181503.3(EXOSC8):c.321G>A (p.Gln107=) rs1127446 0.32239
NM_020320.5(RARS2):c.451+140G>A rs34513746 0.32228
NM_001759.4(CCND2):c.570C>G (p.Thr190=) rs3217805 0.31575
NM_001135146.2(SLC39A8):c.552+48C>T rs1462947 0.30373
NM_001128159.3(VPS53):c.1117-91C>G rs7225041 0.30116
NM_021926.4(ALX4):c.1074C>T (p.His358=) rs3802805 0.29957
NM_005559.4(LAMA1):c.6227T>C (p.Ile2076Thr) rs671871 0.29406
NM_004958.4(MTOR):c.5553C>T (p.Ser1851=) rs2275527 0.29172
NM_004958.4(MTOR):c.6909G>A (p.Leu2303=) rs11121691 0.28827
NM_014875.3(KIF14):c.4897C>G (p.Pro1633Ala) rs12120084 0.28388
NM_003611.3(OFD1):c.1129+16A>G rs3815049 0.28069
NM_015631.6(TCTN3):c.1204-43T>C rs17461546 0.27142
NM_001378615.1(CC2D2A):c.3595-22C>T rs4280724 0.26375
NM_005559.4(LAMA1):c.3126+7A>G rs603258 0.25992
NM_005559.4(LAMA1):c.8982C>T (p.Asp2994=) rs2016639 0.25393
NM_018082.6(POLR3B):c.3396T>C (p.Asn1132=) rs13561 0.24486
NM_020320.5(RARS2):c.111-21C>T rs9450740 0.24263
NM_018082.6(POLR3B):c.2055T>C (p.Tyr685=) rs10861607 0.22605
NM_016111.4(TELO2):c.2227-39C>T rs3736721 0.22446
NM_015272.5(RPGRIP1L):c.1401+127A>G rs7192060 0.22379
NM_005559.4(LAMA1):c.4729T>G (p.Ser1577Ala) rs12961939 0.21927
NM_015631.6(TCTN3):c.1453-28A>G rs12784530 0.21461
NM_001378615.1(CC2D2A):c.3201G>A (p.Ser1067=) rs73125627 0.20422
NM_005559.4(LAMA1):c.2021A>C (p.Asn674Thr) rs566655 0.20323
NM_015272.5(RPGRIP1L):c.3432+67G>A rs113961478 0.19784
NM_001128159.3(VPS53):c.219-11T>C rs4968100 0.19527
NM_033026.6(PCLO):c.860A>G (p.Asp287Gly) rs61741659 0.18909
NM_000435.3(NOTCH3):c.303C>T (p.Thr101=) rs3815188 0.18114
NM_001128159.3(VPS53):c.81C>T (p.Ile27=) rs11558129 0.16882
NM_005559.4(LAMA1):c.4026T>G (p.Val1342=) rs73938538 0.15758
NM_001128159.3(VPS53):c.1867-71T>C rs12951098 0.15268
NM_015272.5(RPGRIP1L):c.3428C>G (p.Thr1143Ser) rs111775292 0.14328
NM_005559.4(LAMA1):c.5288C>T (p.Ala1763Val) rs12607841 0.13777
NM_001378615.1(CC2D2A):c.2182-24C>T rs2041673 0.13698
NM_001082486.2(ACD):c.1298+20C>A rs67114979 0.13128
NM_001378615.1(CC2D2A):c.2830-38G>T rs35309200 0.12892
NM_005559.4(LAMA1):c.6345+7T>C rs10164200 0.12418
NM_001082486.2(ACD):c.413+3A>G rs8058187 0.12302
NM_020320.5(RARS2):c.1704A>G (p.Lys568=) rs8802 0.12189
NM_015272.5(RPGRIP1L):c.3936C>T (p.Asp1312=) rs4784320 0.10935
NM_015272.5(RPGRIP1L):c.3073G>A (p.Gly1025Ser) rs2111119 0.10881
NM_207346.3(TSEN54):c.409A>C (p.Ile137Leu) rs11559205 0.09934
NM_001368809.2(AMPD2):c.91+180C>G rs186745159 0.09427
NM_001368809.2(AMPD2):c.-263+18T>C rs28362580 0.09386
NM_020320.5(RARS2):c.872A>G (p.Lys291Arg) rs17850652 0.09110
NM_178161.3(PTF1A):c.*15G>A rs10828415 0.08608
NM_003384.3(VRK1):c.1159+43C>G rs45457797 0.08564
NM_021926.4(ALX4):c.778-11G>A rs75147697 0.08417
NM_017777.4(MKS1):c.1024+128C>T rs72839966 0.08242
NM_001128159.3(VPS53):c.1117-3C>T rs56807006 0.08020
NM_016955.4(SEPSECS):c.1356G>C (p.Lys452Asn) rs2302566 0.07763
NM_020320.5(RARS2):c.111-19T>G rs6900057 0.07559
NM_017777.4(MKS1):c.191-44G>A rs73329636 0.06658
NM_020320.5(RARS2):c.974+90T>C rs2273131 0.06641
NM_020320.5(RARS2):c.975-43G>A rs3757371 0.06627
NM_020320.5(RARS2):c.1305+18C>T rs3734908 0.06626
NM_001497.4(B4GALT1):c.597C>T (p.His199=) rs1065765 0.05834
NM_015272.5(RPGRIP1L):c.685G>A (p.Ala229Thr) rs61747071 0.04969
NM_015272.5(RPGRIP1L):c.530-29G>A rs74393433 0.04932
NM_207346.3(TSEN54):c.1447C>G (p.Pro483Ala) rs62088470 0.04801
NM_015272.5(RPGRIP1L):c.3790G>A (p.Asp1264Asn) rs3213758 0.04663
NM_016955.4(SEPSECS):c.1211+7A>G rs17408685 0.04557
NM_020320.5(RARS2):c.1237+38G>A rs13203056 0.04243
NM_005027.4(PIK3R2):c.2179G>A (p.Ala727Thr) rs149081991 0.03942
NM_001082486.2(ACD):c.1371G>T (p.Pro457=) rs14920 0.03535
NM_020320.5(RARS2):c.703G>A (p.Val235Met) rs35862137 0.03019
NM_015272.5(RPGRIP1L):c.2231G>A (p.Arg744Gln) rs2302677 0.02738
NM_001368809.2(AMPD2):c.1984-19C>T rs75276578 0.02404
NM_015272.5(RPGRIP1L):c.1341G>A (p.Leu447=) rs61743997 0.02188
NM_001368809.2(AMPD2):c.1104G>A (p.Ser368=) rs34030799 0.01484
NM_001082486.2(ACD):c.923G>A (p.Gly308Glu) rs147189192 0.00679
NM_014008.5(CCDC22):c.1288G>A (p.Ala430Thr) rs144632022 0.00602
NM_001082486.2(ACD):c.1207-10C>T rs67185288 0.00536
NM_001082486.2(ACD):c.494-20C>T rs59443695 0.00465
NM_001173990.3(TMEM216):c.35-17C>T rs147953784 0.00450
NM_001368809.2(AMPD2):c.1716C>T (p.Ser572=) rs116415979 0.00302
NM_004958.4(MTOR):c.6624T>C (p.Leu2208=) rs56051835 0.00258
NM_001082486.2(ACD):c.819C>T (p.Pro273=) rs138740815 0.00251
NM_001082486.2(ACD):c.1336C>T (p.Leu446=) rs1050346 0.00188
NM_001128159.3(VPS53):c.2062A>G (p.Ile688Val) rs140376049 0.00139
NM_001082486.2(ACD):c.80G>A (p.Arg27Gln) rs142507451 0.00135
NM_001082486.2(ACD):c.132C>T (p.Gly44=) rs138527794 0.00102
NM_001368809.2(AMPD2):c.1408-12C>T rs189047791 0.00090
NM_001368809.2(AMPD2):c.1080+9T>C rs202160763 0.00010
NM_000435.3(NOTCH3):c.5913+45T>C rs4809028
NM_001128159.3(VPS53):c.1218+57G>C rs10521105
NM_001128159.3(VPS53):c.1314-19dup rs36070043
NM_001134831.2(AHI1):c.2037-77G>A rs737561
NM_001173990.3(TMEM216):c.432-1G>C rs10897158
NM_001173990.3:c.432-11_432-10insA
NM_001199198.3(TBC1D23):c.1554-49dup rs2148869399
NM_001368809.2(AMPD2):c.2475A>G (p.Gln825=) rs553448801
NM_001378615.1(CC2D2A):c.40-122A>C rs9993580
NM_003611.3(OFD1):c.1412-11del rs36052228
NM_005559.4(LAMA1):c.4479A>G (p.Ser1493=) rs625106
NM_014008.5(CCDC22):c.747= (p.Gln249=) rs2294020
NM_016111.4(TELO2):c.2407+77A>T rs12927760
NM_016111.4(TELO2):c.933+11del rs11344586
NM_025114.4(CEP290):c.2268A>G (p.Ser756=) rs2468255
NM_025114.4(CEP290):c.3574-9del rs10717563
NM_025114.4(CEP290):c.6522+5dup rs11405846
NM_033026.6(PCLO):c.8778_8780dup (p.Asp2926dup) rs10630259

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.