ClinVar Miner

List of variants reported as benign for central nervous system malformation by Invitae

Included ClinVar conditions (163):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 240
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_014846.4(WASHC5):c.2770+18_2770+19insG rs11370883 0.99994
NM_005027.4(PIK3R2):c.937T>C (p.Ser313Pro) rs1011320 0.95640
NM_005027.4(PIK3R2):c.700A>C (p.Ser234Arg) rs2241088 0.93443
NM_005027.4(PIK3R2):c.1911T>C (p.Ser637=) rs273269 0.85598
NM_002449.5(MSX2):c.386T>C (p.Met129Thr) rs4242182 0.78320
NM_001368809.2(AMPD2):c.860+19A>G rs524998 0.73896
NM_001368809.2(AMPD2):c.1272T>C (p.His424=) rs863978 0.70414
NM_001082486.2(ACD):c.1295T>C (p.Val432Ala) rs6979 0.60624
NM_016042.4(EXOSC3):c.498G>A (p.Gln166=) rs7158 0.53959
NM_015631.6(TCTN3):c.603T>A (p.Thr201=) rs10786229 0.35079
NM_003384.3(VRK1):c.705C>T (p.Gly235=) rs2230532 0.32707
NM_003384.3(VRK1):c.45A>G (p.Ala15=) rs2145635 0.32398
NM_001077418.3(TMEM231):c.582+17T>A rs2738801 0.27293
NM_001077418.3(TMEM231):c.-6G>C rs3743602 0.21908
NM_015631.6(TCTN3):c.500-11A>T rs11188434 0.18618
NM_014846.4(WASHC5):c.979-20C>T rs12546285 0.18463
NM_022836.4(DCLRE1B):c.234T>C (p.His78=) rs3761936 0.15394
NM_014846.4(WASHC5):c.3291G>A (p.Ala1097=) rs11542889 0.14383
NM_014846.4(WASHC5):c.187-3C>T rs16900368 0.13363
NM_014846.4(WASHC5):c.417+11A>G rs2384917 0.13320
NM_001082486.2(ACD):c.1298+20C>A rs67114979 0.13128
NM_001368809.2(AMPD2):c.82G>A (p.Ala28Thr) rs28362581 0.13084
NM_001082486.2(ACD):c.413+3A>G rs8058187 0.12302
NM_014846.4(WASHC5):c.1764+12A>G rs3765213 0.11313
NM_001077418.3(TMEM231):c.16C>G (p.Leu6Val) rs3743601 0.10494
NM_015631.6(TCTN3):c.193A>C (p.Thr65Pro) rs11553577 0.10199
NM_001077418.3(TMEM231):c.813G>A (p.Val271=) rs2242406 0.08287
NM_001044385.3(TMEM237):c.1096G>T (p.Ala366Ser) rs73989521 0.07946
NM_005027.4(PIK3R2):c.700= (p.Ser234=) rs2241088 0.06557
NM_016042.4(EXOSC3):c.673T>C (p.Tyr225His) rs3208406 0.06407
NM_005027.4(PIK3R2):c.2127C>T (p.Thr709=) rs112813367 0.04637
NM_005027.4(PIK3R2):c.937= (p.Ser313=) rs1011320 0.04360
NM_005027.4(PIK3R2):c.2179G>A (p.Ala727Thr) rs149081991 0.03942
NM_005027.4(PIK3R2):c.903G>A (p.Ala301=) rs28730848 0.03689
NM_001082486.2(ACD):c.1371G>T (p.Pro457=) rs14920 0.03535
NM_014846.4(WASHC5):c.186+17G>A rs59134934 0.03280
NC_000016.10:g.67660703A>G rs72547496 0.03001
NM_014846.4(WASHC5):c.1408+7A>G rs16900312 0.02845
NM_014846.4(WASHC5):c.1151-8G>A rs16900335 0.02839
NM_014846.4(WASHC5):c.1245A>G (p.Leu415=) rs10429323 0.02837
NM_001368809.2(AMPD2):c.1984-19C>T rs75276578 0.02404
NM_014846.4(WASHC5):c.597A>G (p.Pro199=) rs7812319 0.02380
NM_001044385.3(TMEM237):c.9T>G (p.Thr3=) rs6736435 0.02349
NM_001077418.3(TMEM231):c.582+8C>G rs144252983 0.02257
NM_001044385.3(TMEM237):c.395+7A>G rs78297522 0.01932
NM_016464.5(TMEM138):c.261G>A (p.Val87=) rs35245221 0.01861
NM_001077418.3(TMEM231):c.582+3A>G rs114290622 0.01823
NM_001368809.2(AMPD2):c.1104G>A (p.Ser368=) rs34030799 0.01484
NM_022836.4(DCLRE1B):c.1384G>A (p.Asp462Asn) rs28381079 0.01483
NM_015631.6(TCTN3):c.925G>T (p.Ala309Ser) rs55859130 0.01420
NM_014846.4(WASHC5):c.3225A>G (p.Pro1075=) rs34569226 0.01390
NM_001077418.3(TMEM231):c.177G>C (p.Pro59=) rs78196225 0.01307
NM_005027.4(PIK3R2):c.2080C>T (p.Leu694=) rs116321373 0.01259
NM_005027.4(PIK3R2):c.2163C>T (p.Pro721=) rs147625988 0.00840
NM_005027.4(PIK3R2):c.291C>T (p.Pro97=) rs201655779 0.00768
NM_001044385.3(TMEM237):c.75-13T>C rs116829037 0.00764
NM_018718.3(CEP41):c.718T>G (p.Cys240Gly) rs113941736 0.00760
NM_005027.4(PIK3R2):c.1736+12C>T rs112411913 0.00759
NM_001368809.2(AMPD2):c.223-4C>T rs116223306 0.00736
NM_005027.4(PIK3R2):c.415+18dup rs200295171 0.00686
NM_001082486.2(ACD):c.923G>A (p.Gly308Glu) rs147189192 0.00679
NM_014846.4(WASHC5):c.3319G>A (p.Val1107Met) rs138407503 0.00618
NM_001082486.1(ACD):c.162C>T (p.Pro54=) rs73597595 0.00544
NM_015631.6(TCTN3):c.630T>C (p.Ala210=) rs41299157 0.00543
NM_001082486.2(ACD):c.1207-10C>T rs67185288 0.00536
NM_001082486.2(ACD):c.801C>T (p.Ala267=) rs72549181 0.00530
NM_001044385.3(TMEM237):c.80-11T>C rs76296365 0.00503
NM_014846.4(WASHC5):c.867A>C (p.Val289=) rs79464415 0.00491
NM_001077418.3(TMEM231):c.498G>A (p.Pro166=) rs201636741 0.00468
NM_001082486.2(ACD):c.494-20C>T rs59443695 0.00465
NM_005027.4(PIK3R2):c.1560-17C>T rs183117011 0.00461
NM_018718.3(CEP41):c.208-5A>G rs11765434 0.00453
NM_005027.4(PIK3R2):c.451C>T (p.Pro151Ser) rs143873873 0.00450
NM_015631.6(TCTN3):c.1030G>A (p.Gly344Arg) rs141088838 0.00423
NM_015631.6(TCTN3):c.224C>T (p.Ala75Val) rs41291570 0.00421
NM_016042.4(EXOSC3):c.540T>C (p.Cys180=) rs62640003 0.00417
NM_001077418.3(TMEM231):c.891G>A (p.Val297=) rs149888762 0.00375
NM_002601.4(PDE6D):c.371+8A>C rs75242814 0.00367
NM_014846.4(WASHC5):c.2100G>A (p.Val700=) rs148936723 0.00357
NM_005465.7(AKT3):c.1416C>G (p.Ser472=) rs148332912 0.00352
NM_015631.6(TCTN3):c.21G>A (p.Ala7=) rs61737888 0.00320
NM_001368809.2(AMPD2):c.1242C>T (p.Tyr414=) rs114727970 0.00316
NM_001368809.2(AMPD2):c.1716C>T (p.Ser572=) rs116415979 0.00302
NM_001082486.2(ACD):c.819C>T (p.Pro273=) rs138740815 0.00251
NM_005027.4(PIK3R2):c.160G>A (p.Val54Met) rs201370957 0.00242
NM_005027.4(PIK3R2):c.1643C>T (p.Ala548Val) rs10413655 0.00240
NM_001044385.3(TMEM237):c.136+8G>A rs200618675 0.00220
NM_018718.3(CEP41):c.616C>G (p.Pro206Ala) rs143303575 0.00218
NM_001044385.3(TMEM237):c.554-15G>A rs144051344 0.00213
NM_001044385.3(TMEM237):c.1134T>C (p.Tyr378=) rs77570029 0.00211
NM_001044385.3(TMEM237):c.396-14C>T rs74411816 0.00210
NM_022836.4(DCLRE1B):c.1302C>T (p.His434=) rs144843243 0.00192
NM_001368809.2(AMPD2):c.708T>G (p.Pro236=) rs114624650 0.00189
NM_001082486.2(ACD):c.1336C>T (p.Leu446=) rs1050346 0.00188
NM_018718.3(CEP41):c.575-12T>C rs186638258 0.00185
NM_001077418.3(TMEM231):c.91G>A (p.Ala31Thr) rs202215735 0.00182
NM_014846.4(WASHC5):c.2771-7T>C rs142685897 0.00181
NM_001368809.2(AMPD2):c.1984-15C>G rs368592941 0.00168
NM_001044385.3(TMEM237):c.348G>A (p.Ala116=) rs191125006 0.00163
NM_001368809.2(AMPD2):c.1587C>A (p.Thr529=) rs35337955 0.00159
NM_014846.4(WASHC5):c.1818C>T (p.Pro606=) rs140063111 0.00156
NM_001368809.2(AMPD2):c.1276-20A>G rs140464475 0.00149
NM_001077418.3(TMEM231):c.804C>T (p.Phe268=) rs149118721 0.00144
NM_005465.7(AKT3):c.1359T>C (p.Asp453=) rs142844303 0.00141
NM_001082486.2(ACD):c.80G>A (p.Arg27Gln) rs142507451 0.00135
NM_005027.4(PIK3R2):c.1416+11C>T rs140187437 0.00133
NM_014846.4(WASHC5):c.2485C>T (p.Leu829=) rs80242901 0.00128
NM_014846.4(WASHC5):c.655G>A (p.Glu219Lys) rs143719918 0.00127
NM_022836.4(DCLRE1B):c.1528A>T (p.Asn510Tyr) rs35397235 0.00126
NM_001044385.3(TMEM237):c.1065C>G (p.Leu355=) rs149240122 0.00111
NM_015631.6(TCTN3):c.1591-5C>T rs181107730 0.00109
NM_005027.4(PIK3R2):c.1953G>A (p.Gln651=) rs112859649 0.00108
NM_014846.4(WASHC5):c.1346G>A (p.Arg449Gln) rs202165114 0.00108
NM_001082486.2(ACD):c.132C>T (p.Gly44=) rs138527794 0.00102
NM_001368809.2(AMPD2):c.855C>T (p.Asp285=) rs114463063 0.00101
NM_002449.5(MSX2):c.117C>T (p.Arg39=) rs376630472 0.00097
NM_001082486.2(ACD):c.444C>T (p.Leu148=) rs151132164 0.00096
NM_005027.4(PIK3R2):c.691C>T (p.Arg231Cys) rs558127851 0.00095
NM_001368809.2(AMPD2):c.1408-12C>T rs189047791 0.00090
NM_001077418.3(TMEM231):c.900T>C (p.Ile300=) rs199628375 0.00089
NM_014846.4(WASHC5):c.1187A>G (p.Lys396Arg) rs142423043 0.00086
NM_003384.3(VRK1):c.286+12A>G rs376603491 0.00085
NM_014846.4(WASHC5):c.1029A>G (p.Gln343=) rs140523354 0.00083
NM_005027.4(PIK3R2):c.10C>T (p.Pro4Ser) rs142933317 0.00080
NM_014846.4(WASHC5):c.1605C>T (p.Ile535=) rs143654828 0.00080
NM_005027.4(PIK3R2):c.1938C>T (p.Ile646=) rs146987351 0.00079
NM_014846.4(WASHC5):c.732G>A (p.Pro244=) rs146320386 0.00079
NM_001077418.3(TMEM231):c.471G>A (p.Ala157=) rs375273015 0.00077
NM_005027.4(PIK3R2):c.1416+15G>A rs202218011 0.00076
NM_015631.6(TCTN3):c.500-6T>C rs201444392 0.00076
NM_003384.3(VRK1):c.1020C>T (p.Asp340=) rs147853760 0.00066
NM_005027.4(PIK3R2):c.843G>A (p.Ala281=) rs140686003 0.00052
NM_003384.3(VRK1):c.375-8G>C rs191021502 0.00051
NM_005465.7(AKT3):c.285-13C>T rs201603638 0.00051
NM_005027.4(PIK3R2):c.2168C>T (p.Pro723Leu) rs201029925 0.00048
NM_005465.7(AKT3):c.807C>T (p.Tyr269=) rs150205993 0.00044
NM_005027.4(PIK3R2):c.1809-17A>G rs199501065 0.00040
NM_005465.7(AKT3):c.792C>T (p.Ser264=) rs77764554 0.00039
NM_014846.4(WASHC5):c.2668-19C>T rs368313044 0.00038
NM_001082486.2(ACD):c.99+18G>A rs369046068 0.00036
NM_005027.4(PIK3R2):c.323-15del rs573541270 0.00036
NM_005465.7(AKT3):c.46+12G>A rs184404650 0.00036
NM_016464.5(TMEM138):c.216C>T (p.Asn72=) rs145939072 0.00035
NM_001044385.3(TMEM237):c.475A>G (p.Thr159Ala) rs199500256 0.00034
NM_001368809.2(AMPD2):c.532-18G>A rs41314005 0.00032
NM_005027.4(PIK3R2):c.1986C>T (p.Asp662=) rs749028997 0.00031
NM_005027.4(PIK3R2):c.302G>A (p.Arg101His) rs367971686 0.00031
NM_015631.6(TCTN3):c.889-8G>A rs374331871 0.00029
NM_005027.4(PIK3R2):c.104G>A (p.Arg35Gln) rs762238231 0.00028
NM_014846.4(WASHC5):c.12T>C (p.Phe4=) rs202120400 0.00028
NM_016464.5(TMEM138):c.327C>T (p.Ser109=) rs201318247 0.00028
NM_005027.4(PIK3R2):c.323-16_323-15del rs374033727 0.00025
NM_016042.4(EXOSC3):c.166A>C (p.Asn56His) rs148348866 0.00022
NM_001368809.2(AMPD2):c.1846T>C (p.Leu616=) rs757521991 0.00021
NM_001077418.3(TMEM231):c.140-28C>G rs375353411 0.00019
NM_001044385.3(TMEM237):c.869+10A>G rs376868416 0.00016
NM_003384.3(VRK1):c.710-13C>T rs374386994 0.00016
NM_014846.4(WASHC5):c.2199+4C>A rs145721086 0.00016
NM_001368809.2(AMPD2):c.912C>T (p.Asp304=) rs141396033 0.00015
NM_005027.4(PIK3R2):c.1011-19A>G rs373122934 0.00015
NM_005465.7(AKT3):c.1398G>A (p.Pro466=) rs150573714 0.00015
NM_001368809.2(AMPD2):c.1080+9T>C rs202160763 0.00010
NM_002449.5(MSX2):c.699G>A (p.Ala233=) rs201880865 0.00008
NM_015631.6(TCTN3):c.933G>T (p.Leu311=) rs371380545 0.00008
NM_001077418.3(TMEM231):c.376C>T (p.Leu126=) rs557695110 0.00007
NM_015631.6(TCTN3):c.1278A>G (p.Ala426=) rs184805842 0.00007
NM_001368809.2(AMPD2):c.2158-9C>A rs756915998 0.00006
NM_018718.3(CEP41):c.320C>G (p.Ala107Gly) rs141025803 0.00006
NM_005027.4(PIK3R2):c.1076G>C (p.Ser359Thr) rs1041937206 0.00005
NM_001044385.3(TMEM237):c.274+11A>G rs200487330 0.00004
NM_001044385.3(TMEM237):c.33G>A (p.Glu11=) rs544767440 0.00004
NM_002449.5(MSX2):c.49G>A (p.Gly17Ser) rs754789827 0.00004
NM_002449.5(MSX2):c.723G>A (p.Pro241=) rs201103544 0.00004
NM_005027.4(PIK3R2):c.1215C>T (p.Tyr405=) rs200914853 0.00004
NM_016042.4(EXOSC3):c.294T>A (p.Gly98=) rs910605187 0.00004
NM_016464.5(TMEM138):c.387G>A (p.Leu129=) rs553815473 0.00004
NM_001044385.3(TMEM237):c.396-13G>A rs570600190 0.00003
NM_001368809.2(AMPD2):c.-52C>G rs570541266 0.00003
NM_005027.4(PIK3R2):c.1620G>A (p.Thr540=) rs546014325 0.00003
NM_001044385.3(TMEM237):c.74+16A>G rs538615771 0.00002
NM_005027.4(PIK3R2):c.304G>A (p.Asp102Asn) rs774502328 0.00002
NM_005465.7(AKT3):c.1163+16C>T rs781443210 0.00002
NM_002449.5(MSX2):c.756G>A (p.Val252=) rs542254664 0.00001
NM_005027.4(PIK3R2):c.2171C>T (p.Pro724Leu) rs1239460949 0.00001
NM_005027.4(PIK3R2):c.311C>A (p.Ala104Asp) rs770694944 0.00001
NM_005465.7(AKT3):c.1044C>T (p.Asn348=) rs199771220 0.00001
NM_015631.6(TCTN3):c.324C>T (p.Asp108=) rs566756038 0.00001
NC_000016.9:g.(?_75573892)_(75575373_?)dup
NC_000016.9:g.(?_75573892)_(75576601_?)dup
NM_001044385.3(TMEM237):c.1159+17del rs766664373
NM_001044385.3(TMEM237):c.1159+17dup
NM_001044385.3(TMEM237):c.678-20_678-17del rs754336127
NM_001044385.3(TMEM237):c.80-18dup rs747217784
NM_001044385.3(TMEM237):c.870-13_870-12del rs555284377
NM_001082486.2(ACD):c.743-3dup rs1369632476
NM_001368809.2(AMPD2):c.1005T>C (p.His335=)
NM_001368809.2(AMPD2):c.1863-3dup
NM_001368809.2(AMPD2):c.2475A>G (p.Gln825=) rs553448801
NM_002449.5(MSX2):c.380-18C>T
NM_002449.5(MSX2):c.444C>T (p.Pro148=)
NM_003384.3(VRK1):c.1160-8del rs2139857568
NM_003384.3(VRK1):c.161-7dup rs1295596727
NM_003384.3(VRK1):c.374+7dup
NM_003384.3(VRK1):c.375-14A>G
NM_003384.3(VRK1):c.483+20_483+22del rs566207500
NM_005027.4(PIK3R2):c.1002C>G (p.Asp334Glu)
NM_005027.4(PIK3R2):c.1110-16C>T
NM_005027.4(PIK3R2):c.1329C>A (p.Gly443=) rs199931960
NM_005027.4(PIK3R2):c.1416+14C>T
NM_005027.4(PIK3R2):c.154C>A (p.Gln52Lys)
NM_005027.4(PIK3R2):c.1615C>T (p.Arg539Cys)
NM_005027.4(PIK3R2):c.1676G>A (p.Arg559His)
NM_005027.4(PIK3R2):c.1682A>G (p.Asn561Ser) rs769397940
NM_005027.4(PIK3R2):c.1809-7A>T rs201271257
NM_005027.4(PIK3R2):c.1809-8dup rs566994275
NM_005027.4(PIK3R2):c.1845G>A (p.Pro615=) rs201568661
NM_005027.4(PIK3R2):c.1875C>T (p.Gly625=) rs1258315228
NM_005027.4(PIK3R2):c.2146G>C (p.Val716Leu)
NM_005027.4(PIK3R2):c.46C>T (p.Arg16Cys) rs80233027
NM_005027.4(PIK3R2):c.500C>T (p.Thr167Met)
NM_005027.4(PIK3R2):c.598+11C>T
NM_005027.4(PIK3R2):c.694G>A (p.Val232Met)
NM_005465.7(AKT3):c.1251+15T>C
NM_005465.7(AKT3):c.173-23_173-20del rs773557899
NM_005465.7(AKT3):c.430-17dup rs780927904
NM_005465.7(AKT3):c.46+11C>T
NM_005465.7(AKT3):c.628-9dup
NM_014846.4(WASHC5):c.187-6dup rs745362878
NM_014846.4(WASHC5):c.2851-18del
NM_014846.4(WASHC5):c.333-19A>G rs2384916
NM_014846.4(WASHC5):c.333-19A>T
NM_014846.4(WASHC5):c.711+16A>G
NM_014846.4(WASHC5):c.720G>A (p.Ala240=) rs758215702
NM_015631.6(TCTN3):c.211G>T (p.Val71Leu) rs138495428
NM_016042.4(EXOSC3):c.810C>T (p.Ser270=)
NM_016042.4(EXOSC3):c.814T>C (p.Leu272=)
NM_016464.5(TMEM138):c.129-11dup
NM_018718.3(CEP41):c.278-15A>T rs142452124
NM_018718.3(CEP41):c.575-14del rs144531086
NM_018718.3(CEP41):c.758-14dup rs1156468685

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