ClinVar Miner

List of variants reported as likely benign for central nervous system malformation by Illumina Laboratory Services, Illumina

Included ClinVar conditions (164):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 247
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001232.4(CASQ2):c.*632G>C rs1140238 0.65651
NM_001232.4(CASQ2):c.*482C>T rs7521023 0.63558
NM_001232.4(CASQ2):c.1185C>T (p.Asp395=) rs7413162 0.39681
NM_138959.3(VANGL1):c.*1183del rs3841008 0.25316
NM_001232.4(CASQ2):c.*1123_*1124del rs56839330 0.23414
NM_020320.5(RARS2):c.1704A>G (p.Lys568=) rs8802 0.12189
NM_006416.5(SLC35A1):c.887-14T>C rs56136150 0.10768
NM_001232.4(CASQ2):c.*138T>C rs28730710 0.10658
NM_025265.4(TSEN2):c.-391G>A rs3806662 0.09194
NM_016955.4(SEPSECS):c.*455C>T rs73252520 0.08857
NM_016955.4(SEPSECS):c.*2694A>G rs956925 0.07936
NM_207346.3(TSEN54):c.3_8dup (p.2_3EP[4]) rs398124622 0.06994
NM_001232.4(CASQ2):c.1194T>C (p.Asp398=) rs28730711 0.04871
NM_178161.3(PTF1A):c.*190C>T rs74121767 0.04559
NM_024075.4(TSEN34):c.*1177G>T rs78711269 0.03779
NM_006416.5(SLC35A1):c.*147C>T rs55960393 0.03465
NM_153240.5(NPHP3):c.*266G>A rs11708200 0.03396
NM_153240.5(NPHP3):c.2571-7T>C rs62292468 0.02974
NM_207346.2(TSEN54):c.*331T>A rs150621720 0.02560
NM_153240.5(NPHP3):c.*785G>A rs6774366 0.02518
NM_024075.4(TSEN34):c.*1176A>T rs78793520 0.02245
NM_001232.4(CASQ2):c.1014+9C>T rs77775029 0.02121
NM_001232.4(CASQ2):c.1005T>C (p.Asn335=) rs28730712 0.02116
NM_016955.4(SEPSECS):c.*638G>C rs10004441 0.01839
NM_016955.4(SEPSECS):c.*2209A>G rs9998044 0.01837
NM_153240.5(NPHP3):c.864T>A (p.Thr288=) rs147932449 0.01825
NM_153240.5(NPHP3):c.3913C>T (p.Arg1305Cys) rs35485382 0.01709
NM_138959.3(VANGL1):c.*3544C>T rs74117023 0.01618
NM_153240.5(NPHP3):c.1986G>A (p.Arg662=) rs77533254 0.01496
NM_138959.3(VANGL1):c.*3336G>A rs61732170 0.01470
NM_006416.5(SLC35A1):c.*240G>T rs9450722 0.01462
NM_001044385.3(TMEM237):c.*3124A>T rs79378497 0.01390
NM_020320.5(RARS2):c.63A>G (p.Pro21=) rs7748563 0.01309
NM_153240.5(NPHP3):c.57G>C (p.Thr19=) rs192633696 0.01128
NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr) rs145643112 0.01037
NM_016955.4(SEPSECS):c.*1041T>C rs114420733 0.01027
NM_016955.4(SEPSECS):c.*371_*372del rs143987218 0.01024
NM_153240.5(NPHP3):c.450G>A (p.Ala150=) rs78527322 0.00906
NM_025114.4(CEP290):c.-33G>T rs139415563 0.00894
NM_015272.5(RPGRIP1L):c.3548C>G (p.Ala1183Gly) rs139974543 0.00854
NM_138959.3(VANGL1):c.-239G>A rs563855412 0.00806
NM_018718.3(CEP41):c.718T>G (p.Cys240Gly) rs113941736 0.00760
NM_138959.3(VANGL1):c.*1652C>T rs146512242 0.00738
NM_015272.5(RPGRIP1L):c.3372C>T (p.Ser1124=) rs146902870 0.00702
NM_018718.3(CEP41):c.*1512C>T rs73721889 0.00689
NM_153240.5(NPHP3):c.3941G>C (p.Ser1314Thr) rs75316802 0.00658
NM_021926.4(ALX4):c.*290T>C rs7128671 0.00637
NM_001173990.3(TMEM216):c.*21A>G rs111371929 0.00615
NM_018082.6(POLR3B):c.1958A>T (p.Asp653Val) rs144161033 0.00581
NM_015272.5(RPGRIP1L):c.2925A>G (p.Val975=) rs144313291 0.00524
NM_015272.5(RPGRIP1L):c.1165A>G (p.Ile389Val) rs79708859 0.00517
NM_001044385.3(TMEM237):c.80-11T>C rs76296365 0.00503
NM_024075.5(TSEN34):c.-5+15G>A rs141003293 0.00497
NM_025114.4(CEP290):c.6401T>C (p.Ile2134Thr) rs117852025 0.00488
NM_018082.6(POLR3B):c.975A>G (p.Glu325=) rs145542203 0.00487
NM_138959.3(VANGL1):c.*5444C>G rs142497673 0.00486
NM_001134831.2(AHI1):c.2798A>G (p.Tyr933Cys) rs41288013 0.00466
NM_003384.2(VRK1):c.-110C>T rs77630815 0.00455
NM_018718.3(CEP41):c.208-5A>G rs11765434 0.00453
NM_138959.3(VANGL1):c.435T>C (p.Cys145=) rs34768472 0.00443
NM_138959.3(VANGL1):c.*3653C>T rs146435279 0.00442
NM_001134831.2(AHI1):c.2972G>A (p.Arg991His) rs35851478 0.00429
NM_001077446.4(TSEN34):c.*1053G>A rs182704571 0.00428
NM_138959.3(VANGL1):c.*2865A>G rs114921471 0.00424
NM_001044385.3(TMEM237):c.*3453T>G rs77771615 0.00420
NM_001044385.3(TMEM237):c.*2137A>G rs115353606 0.00418
NM_001044385.3(TMEM237):c.*2349C>T rs74884418 0.00418
NM_001044385.3(TMEM237):c.*3372C>T rs192214909 0.00418
NM_001044385.3(TMEM237):c.*1107C>T rs143516209 0.00417
NM_001044385.3(TMEM237):c.*1975C>G rs142233268 0.00417
NM_001044385.3(TMEM237):c.*2719G>A rs142852956 0.00417
NM_001044385.3(TMEM237):c.*2180G>A rs77649251 0.00416
NM_138959.3(VANGL1):c.345C>T (p.Val115=) rs79828493 0.00413
NM_001044385.3(TMEM237):c.*1588G>A rs150141936 0.00396
NM_024075.5(TSEN34):c.-95A>G rs115290127 0.00390
NM_001134831.2(AHI1):c.2505G>A (p.Arg835=) rs41288017 0.00383
NM_001044385.3(TMEM237):c.*2431T>G rs142355657 0.00379
NM_000368.5(TSC1):c.1342C>T (p.Pro448Ser) rs118203518 0.00372
NM_025114.4(CEP290):c.1522+6C>T rs148446546 0.00371
NM_025265.4(TSEN2):c.272-4C>G rs41293385 0.00369
NM_001128178.3(NPHP1):c.14G>T (p.Arg5Leu) rs190983114 0.00366
NM_138959.3(VANGL1):c.330C>T (p.Tyr110=) rs41275546 0.00358
NM_025265.4(TSEN2):c.-20G>A rs9871742 0.00345
NM_001044385.3(TMEM237):c.*2480T>G rs75655554 0.00337
NM_016042.4(EXOSC3):c.*881A>G rs143319153 0.00332
NM_025114.4(CEP290):c.5322C>T (p.Leu1774=) rs117370446 0.00329
NM_018082.6(POLR3B):c.2136A>G (p.Leu712=) rs139146614 0.00324
NM_207346.3(TSEN54):c.*169T>C rs111972085 0.00317
NM_001134831.2(AHI1):c.1791C>T (p.Ile597=) rs150425546 0.00307
NM_001134831.2(AHI1):c.724C>T (p.Pro242Ser) rs143522987 0.00307
NM_001378615.1(CC2D2A):c.-87G>A rs145443888 0.00305
NM_016955.4(SEPSECS):c.*3402A>G rs149506792 0.00300
NM_018718.3(CEP41):c.*136T>G rs148305542 0.00287
NM_018718.3(CEP41):c.*4314T>C rs114939029 0.00286
NM_001378615.1(CC2D2A):c.4459C>T (p.Arg1487Cys) rs186486235 0.00265
NM_025265.4(TSEN2):c.-173C>T rs76012118 0.00250
NM_015272.5(RPGRIP1L):c.532A>G (p.Ile178Val) rs140067659 0.00245
NM_020320.5(RARS2):c.-8A>C rs28381459 0.00245
NM_015272.5(RPGRIP1L):c.2807T>G (p.Ile936Ser) rs146197239 0.00244
NM_016042.4(EXOSC3):c.193G>A (p.Val65Ile) rs62640002 0.00231
NM_018718.3(CEP41):c.1009T>C (p.Ser337Pro) rs147444165 0.00223
NM_020320.5(RARS2):c.1410C>A (p.Leu470=) rs139564081 0.00223
NM_001044385.3(TMEM237):c.136+8G>A rs200618675 0.00220
NM_001232.4(CASQ2):c.*143G>A rs28730709 0.00217
NM_021926.4(ALX4):c.*2349C>A rs139570599 0.00210
NM_016042.4(EXOSC3):c.*64C>T rs142727320 0.00209
NM_001044385.3(TMEM237):c.*439G>A rs139374574 0.00208
NM_001044385.3(TMEM237):c.*634C>T rs139016907 0.00207
NM_001128178.3(NPHP1):c.771+59G>A rs143174377 0.00203
NM_138959.3(VANGL1):c.*1772A>G rs114033235 0.00199
NM_015272.5(RPGRIP1L):c.2673G>A (p.Arg891=) rs61742381 0.00195
NM_018082.6(POLR3B):c.1401T>A (p.Gly467=) rs74390456 0.00195
NM_001134831.2(AHI1):c.3039G>A (p.Gln1013=) rs142381345 0.00194
NM_207346.3(TSEN54):c.1167G>C (p.Gln389His) rs369805010 0.00193
NM_025114.4(CEP290):c.3790C>T (p.Arg1264Cys) rs139998038 0.00187
NM_025114.4(CEP290):c.4237G>C (p.Asp1413His) rs183655276 0.00187
NM_001134831.2(AHI1):c.3164C>T (p.Thr1055Met) rs73559947 0.00159
NM_018718.3(CEP41):c.*4594C>T rs151309255 0.00159
NM_015272.5(RPGRIP1L):c.2643T>A (p.Asn881Lys) rs139503476 0.00157
NM_138959.3(VANGL1):c.323A>G (p.Lys108Arg) rs141673853 0.00154
NM_138959.3(VANGL1):c.*383C>G rs75277108 0.00153
NM_153240.5(NPHP3):c.449C>T (p.Ala150Val) rs142663818 0.00142
NM_000368.5(TSC1):c.3103G>A (p.Gly1035Ser) rs118203742 0.00139
NM_016042.4(EXOSC3):c.151C>G (p.Arg51Gly) rs114878910 0.00125
NM_001134831.2(AHI1):c.3257A>G (p.Glu1086Gly) rs148000791 0.00115
NM_021926.4(ALX4):c.*899C>T rs543627488 0.00113
NM_001044385.3(TMEM237):c.1065C>G (p.Leu355=) rs149240122 0.00111
NM_178161.3(PTF1A):c.162C>T (p.Ser54=) rs117678424 0.00110
NM_021926.4(ALX4):c.*3805G>A rs373307279 0.00108
NM_025265.4(TSEN2):c.405G>A (p.Pro135=) rs140728375 0.00090
NM_018082.6(POLR3B):c.1464+14G>A rs200061150 0.00076
NM_000368.5(TSC1):c.273G>A (p.Ser91=) rs115097221 0.00070
NM_207346.3(TSEN54):c.692C>T (p.Pro231Leu) rs141249409 0.00070
NM_021926.4(ALX4):c.1035C>T (p.Ser345=) rs140652481 0.00064
NM_138959.3(VANGL1):c.*2187T>C rs146730302 0.00061
NM_207346.3(TSEN54):c.767G>A (p.Gly256Asp) rs200683263 0.00061
NM_025114.4(CEP290):c.7186G>T (p.Asp2396Tyr) rs189556433 0.00058
NM_021926.4(ALX4):c.917C>T (p.Pro306Leu) rs149897209 0.00052
NM_018718.3(CEP41):c.*2481T>A rs528289176 0.00051
NM_018718.3(CEP41):c.*2896G>A rs147207980 0.00048
NM_018718.3(CEP41):c.*1534T>C rs149912245 0.00047
NM_018718.3(CEP41):c.*1567A>C rs139085191 0.00047
NM_000368.5(TSC1):c.2285A>G (p.Asn762Ser) rs118203670 0.00041
NM_001134831.2(AHI1):c.3342A>G (p.Glu1114=) rs199708272 0.00041
NM_000368.5(TSC1):c.1773G>A (p.Pro591=) rs146578402 0.00040
NM_138959.3(VANGL1):c.*47G>T rs190792695 0.00039
NM_000368.5(TSC1):c.1079C>A (p.Thr360Asn) rs118203493 0.00033
NM_015272.5(RPGRIP1L):c.*1033G>A rs145688122 0.00032
NM_001134831.2(AHI1):c.3418C>T (p.Pro1140Ser) rs201148693 0.00031
NM_021926.4(ALX4):c.1182G>A (p.Ala394=) rs149365713 0.00031
NM_001134831.2(AHI1):c.2589G>A (p.Glu863=) rs147279669 0.00029
NM_018718.3(CEP41):c.*392G>A rs528501184 0.00026
NM_001077446.4(TSEN34):c.314G>A (p.Arg105Gln) rs138586360 0.00024
NM_015272.5(RPGRIP1L):c.1960G>A (p.Glu654Lys) rs141979202 0.00021
NM_000368.5(TSC1):c.1460C>G (p.Ser487Cys) rs118203532 0.00019
NM_018082.6(POLR3B):c.1113T>C (p.Leu371=) rs141885523 0.00019
NM_021926.4(ALX4):c.1149C>T (p.Asn383=) rs376675326 0.00016
NM_021926.4(ALX4):c.188G>A (p.Arg63Gln) rs372830230 0.00016
NM_000368.5(TSC1):c.2209-3T>C rs368309229 0.00014
NM_001173990.2(TMEM216):c.-86G>A rs188478638 0.00014
NM_001378615.1(CC2D2A):c.1830G>A (p.Pro610=) rs185072004 0.00014
NM_016955.4(SEPSECS):c.45G>A (p.Pro15=) rs77226826 0.00014
NM_178161.3(PTF1A):c.102C>T (p.Asp34=) rs199831799 0.00014
NM_001173990.2(TMEM216):c.-135T>C rs183785901 0.00013
NM_018082.6(POLR3B):c.1707T>C (p.Asn569=) rs17038450 0.00013
NM_021926.4(ALX4):c.728C>T (p.Ala243Val) rs145166164 0.00013
NM_000368.5(TSC1):c.1001C>T (p.Ser334Leu) rs118203481 0.00012
NM_000368.5(TSC1):c.2075G>A (p.Arg692Gln) rs199755731 0.00011
NM_001134831.2(AHI1):c.82C>T (p.Arg28Cys) rs199612496 0.00011
NM_001378615.1(CC2D2A):c.717+11T>C rs184351317 0.00011
NM_021926.4(ALX4):c.*563C>T rs574340639 0.00011
NM_001378615.1(CC2D2A):c.2117G>A (p.Arg706Gln) rs778205727 0.00010
NM_178161.3(PTF1A):c.229G>A (p.Ala77Thr) rs549685905 0.00010
NM_000368.5(TSC1):c.1438+6G>A rs118203530 0.00009
NM_001134831.2(AHI1):c.2945G>T (p.Arg982Met) rs370400336 0.00009
NM_001134831.2(AHI1):c.653A>G (p.Tyr218Cys) rs183936286 0.00009
NM_001173990.2(TMEM216):c.-91G>A rs557559653 0.00009
NM_001378615.1(CC2D2A):c.3872T>C (p.Ile1291Thr) rs370492044 0.00009
NM_001378615.1(CC2D2A):c.922T>C (p.Phe308Leu) rs201465430 0.00009
NM_021926.4(ALX4):c.*407G>A rs539799951 0.00009
NM_021926.4(ALX4):c.217C>T (p.Leu73=) rs766525768 0.00009
NM_138959.3(VANGL1):c.1127A>G (p.Gln376Arg) rs200389969 0.00009
NM_207346.3(TSEN54):c.862G>A (p.Val288Ile) rs199682817 0.00009
NM_000368.5(TSC1):c.2209-9C>G rs118203660 0.00007
NM_000368.5(TSC1):c.3387C>T (p.Ala1129=) rs200200869 0.00007
NM_018718.3(CEP41):c.*1336A>G rs781954428 0.00007
NM_000368.5(TSC1):c.1047A>G (p.Pro349=) rs118203492 0.00006
NM_000368.5(TSC1):c.1648C>G (p.Gln550Glu) rs118203553 0.00006
NM_000368.5(TSC1):c.3123C>G (p.Ser1041Arg) rs753374839 0.00006
NM_002449.5(MSX2):c.*1206T>C rs77229212 0.00006
NM_025265.4(TSEN2):c.870A>G (p.Pro290=) rs542708828 0.00006
NM_000368.5(TSC1):c.2696C>G (p.Thr899Ser) rs76801599 0.00005
NM_000368.5(TSC1):c.618T>C (p.His206=) rs118203415 0.00005
NM_021926.4(ALX4):c.*196C>T rs189945537 0.00005
NM_138959.3(VANGL1):c.*707C>T rs562969850 0.00005
NM_000368.5(TSC1):c.2922C>T (p.Leu974=) rs769389702 0.00004
NM_016464.5(TMEM138):c.387G>A (p.Leu129=) rs553815473 0.00004
NM_000368.4(TSC1):c.-242G>T rs571288003 0.00003
NM_000368.5(TSC1):c.2968G>A (p.Glu990Lys) rs200398750 0.00003
NM_000368.5(TSC1):c.3005A>T (p.Asp1002Val) rs202121327 0.00003
NM_000368.5(TSC1):c.3428C>T (p.Pro1143Leu) rs201867031 0.00003
NM_002449.5(MSX2):c.-42C>T rs758437365 0.00003
NM_021926.4(ALX4):c.1218C>T (p.Ala406=) rs745849255 0.00002
NM_000368.5(TSC1):c.168G>A (p.Pro56=) rs781483110 0.00001
NM_000368.5(TSC1):c.2556G>C (p.Leu852=) rs770381040 0.00001
NM_000368.5(TSC1):c.738-10C>A rs768158324 0.00001
NM_000368.5(TSC1):c.772G>A (p.Glu258Lys) rs118203450 0.00001
NM_001128178.3(NPHP1):c.-17G>A rs566875282 0.00001
NM_001128178.3(NPHP1):c.438T>C (p.Asn146=) rs548684868 0.00001
NM_002449.5(MSX2):c.315G>C (p.Lys105Asn) rs760574628 0.00001
NM_020320.5(RARS2):c.660A>C (p.Ala220=) rs553502877 0.00001
NM_021926.4(ALX4):c.*25C>T rs780898515 0.00001
NM_138959.3(VANGL1):c.*2344A>C rs531884184 0.00001
NM_178161.3(PTF1A):c.499G>A (p.Ala167Thr) rs565666569 0.00001
NM_000368.5(TSC1):c.*2228G>A rs528833042
NM_000368.5(TSC1):c.*2893del rs143549363
NM_000368.5(TSC1):c.*295C>A rs113549339
NM_000368.5(TSC1):c.*4631del rs60000611
NM_000368.5(TSC1):c.915G>C (p.Gly305=) rs397515293
NM_001044385.3(TMEM237):c.*2142G>C rs76042698
NM_001044385.3(TMEM237):c.-25G>A rs568671275
NM_001077446.4(TSEN34):c.*385A>T rs36622
NM_001134831.2(AHI1):c.2567C>G (p.Thr856Ser) rs199736888
NM_001173990.3(TMEM216):c.253C>A (p.Arg85=) rs11230683
NM_001173990.3(TMEM216):c.5T>C (p.Leu2Pro) rs569734777
NM_001232.4(CASQ2):c.*1017del rs11347859
NM_001378615.1(CC2D2A):c.1978G>A (p.Val660Ile) rs16892134
NM_002449.5(MSX2):c.*1086dup rs145784193
NM_006416.5(SLC35A1):c.*294dup rs11432150
NM_016042.4(EXOSC3):c.*571TAT[1] rs34753153
NM_016955.3(SEPSECS):c.-147dup rs536637971
NM_016955.4(SEPSECS):c.*236_*237insTTT rs140928773
NM_018082.6(POLR3B):c.1776A>T (p.Leu592=) rs201223367
NM_020320.5(RARS2):c.726A>G (p.Gln242=) rs145499324
NM_021926.4(ALX4):c.*2861C>A rs192487688
NM_021926.4(ALX4):c.*424dup rs113592690
NM_021926.4(ALX4):c.*804AAG[1] rs149719812
NM_025265.4(TSEN2):c.-200C>T rs540294443
NM_025265.4(TSEN2):c.-297C>T rs190941859
NM_025265.4(TSEN2):c.-373C>T rs550947754
NM_025265.4(TSEN2):c.-374G>A rs28657473
NM_138959.3(VANGL1):c.*3762CAAA[2] rs144395099
NM_138959.3(VANGL1):c.*4089del rs138659832
NM_138959.3(VANGL1):c.*4788C>G rs148437823
NM_138959.3(VANGL1):c.*5008T>A rs117347999
NM_138959.3(VANGL1):c.*6763dup rs5777244
NM_207346.3(TSEN54):c.1120C>G (p.Arg374Gly) rs201351319

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