ClinVar Miner

List of variants reported as benign for congenital hypogonadotropic hypogonadism by Illumina Laboratory Services, Illumina

Included ClinVar conditions (68):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 146
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HGVS dbSNP gnomAD frequency
NM_000406.2(GNRHR):c.-224A>G rs2627260 0.97947
NM_025000.4(DCAF17):c.*2340C>T rs888428 0.97908
NM_006261.5(PROP1):c.109+3G>A rs4072924 0.54780
NM_002303.6(LEPR):c.668A>G (p.Gln223Arg) rs1137101 0.50085
NM_017526.5(LEPROT):c.-10T>C rs3790435 0.47981
NM_000406.2(GNRHR):c.-1279G>A rs2062301 0.45906
NM_000406.2(GNRHR):c.-1144T>C rs2062303 0.44562
NM_000406.2(GNRHR):c.-1497C>T rs13138607 0.43890
NM_000406.2(GNRHR):c.-904A>G rs6552113 0.43869
NM_000406.2(GNRHR):c.-1255T>C rs2062302 0.43801
NM_005149.3(TBX19):c.*21T>A rs3885717 0.43776
NM_002303.6(LEPR):c.3057G>A (p.Pro1019=) rs1805096 0.43140
NM_000230.3(LEP):c.*2253C>A rs11761556 0.43092
NM_033343.4(LHX4):c.983A>G (p.Asn328Ser) rs7536561 0.40777
NM_006261.5(PROP1):c.27T>C (p.Ala9=) rs1135320 0.40746
NM_000406.3(GNRHR):c.*2166G>A rs7666201 0.39326
NM_000406.3(GNRHR):c.*829T>C rs17635850 0.39304
NM_000406.3(GNRHR):c.*2496G>A rs1038427 0.38965
NM_000439.5(PCSK1):c.1650T>C (p.Asn550=) rs6233 0.38001
NM_000061.3(BTK):c.1899C>T (p.Cys633=) rs1135363 0.37760
NM_000406.3(GNRHR):c.*2663G>T rs1038426 0.37716
NM_000061.3(BTK):c.*116A>C rs700 0.35507
NM_000306.4(POU1F1):c.*140A>T rs33936108 0.33253
NM_000061.3(BTK):c.*192G>A rs1057403 0.32006
NM_006261.5(PROP1):c.-210A>C rs13187293 0.30465
NM_025000.4(DCAF17):c.150C>T (p.Val50=) rs6751956 0.28531
NM_005149.3(TBX19):c.*251T>C rs1000533 0.26364
NM_002303.6(LEPR):c.326A>G (p.Lys109Arg) rs1137100 0.25399
NM_006261.5(PROP1):c.*354G>A rs4604209 0.24860
NM_025000.4(DCAF17):c.*2795T>C rs17221346 0.24511
NM_000406.3(GNRHR):c.*583A>G rs35845954 0.23514
NM_000406.3(GNRHR):c.*1891T>G rs12508464 0.23503
NM_000406.3(GNRHR):c.*809C>T rs35683646 0.23471
NM_000406.3(GNRHR):c.*802G>C rs35610027 0.23467
NM_178138.6(LHX3):c.79+1975G>A rs2274116 0.23265
NM_000406.3(GNRHR):c.*2055G>A rs17635749 0.22960
NM_000406.3(GNRHR):c.*1260G>T rs13150734 0.22923
NM_000439.5(PCSK1):c.2069G>C (p.Ser690Thr) rs6235 0.22796
NM_006261.5(PROP1):c.424G>A (p.Ala142Thr) rs1800197 0.22589
NM_000439.5(PCSK1):c.-101T>C rs6230 0.20956
NM_000439.5(PCSK1):c.*265T>C rs3811942 0.20188
NM_025000.4(DCAF17):c.322-14C>T rs192861143 0.20151
NM_025000.4(DCAF17):c.*3112C>G rs17221367 0.19832
NM_025000.4(DCAF17):c.999A>G (p.Gln333=) rs3731983 0.19825
NM_025000.4(DCAF17):c.*570G>A rs3795998 0.19821
NM_025000.4(DCAF17):c.*3703A>G rs9789572 0.19820
NM_025000.4(DCAF17):c.*676T>G rs3821084 0.19818
NM_025000.4(DCAF17):c.1267-7C>T rs3731981 0.19769
NM_025000.4(DCAF17):c.*2425T>A rs12151641 0.19764
NM_005149.3(TBX19):c.603+11G>T rs12096093 0.14406
NM_000306.4(POU1F1):c.*139T>A rs4988463 0.14040
NM_000823.4(GHRHR):c.169G>A (p.Ala57Thr) rs4988496 0.12048
NM_000823.4(GHRHR):c.598-10T>C rs35609199 0.10863
NM_033343.4(LHX4):c.778+14G>T rs3806302 0.09243
NM_000406.3(GNRHR):c.453C>T (p.Ser151=) rs4986942 0.08705
NM_006261.5(PROP1):c.*123T>C rs2233788 0.08086
NM_000823.4(GHRHR):c.363G>T (p.Glu121Asp) rs4988498 0.07235
NM_012414.4(RAB3GAP2):c.*404T>C rs1059140 0.06883
NM_012414.4(RAB3GAP2):c.3495G>A (p.Leu1165=) rs11547779 0.06867
NM_012414.4(RAB3GAP2):c.3275G>C (p.Ser1092Thr) rs2289189 0.06844
NM_000823.4(GHRHR):c.-45C>T rs2302021 0.06644
NM_021728.4(OTX2):c.*10G>A rs171978 0.06420
NM_000823.4(GHRHR):c.*221T>C rs28371563 0.05985
NM_033343.4(LHX4):c.452-5T>C rs2764449 0.05703
NM_000823.4(GHRHR):c.366+13T>G rs4988499 0.04905
NM_000823.4(GHRHR):c.564C>T (p.His188=) rs740336 0.04789
NM_012414.4(RAB3GAP2):c.2587A>G (p.Thr863Ala) rs12045447 0.04740
NM_025000.4(DCAF17):c.939G>A (p.Gln313=) rs61731491 0.04289
NM_025000.4(DCAF17):c.*2473G>A rs57999878 0.04194
NM_033343.4(LHX4):c.450C>T (p.Asn150=) rs16855642 0.04109
NM_012414.4(RAB3GAP2):c.*1504G>T rs41303053 0.03924
NM_012414.4(RAB3GAP2):c.713-12T>C rs76473498 0.03857
NM_012414.4(RAB3GAP2):c.2088A>G (p.Thr696=) rs2577126 0.03652
NM_005149.3(TBX19):c.*479G>C rs1003315 0.03197
NM_025000.4(DCAF17):c.555T>A (p.His185Gln) rs3731984 0.03047
NM_025000.4(DCAF17):c.*350G>A rs3795996 0.03008
NM_000823.4(GHRHR):c.1265T>C (p.Met422Thr) rs2228078 0.02812
NM_000061.3(BTK):c.*334T>G rs183674618 0.02721
NM_033343.4(LHX4):c.-120C>T rs355625 0.02332
NM_005149.3(TBX19):c.*26C>G rs143627386 0.02303
NM_005149.3(TBX19):c.*1155C>G rs77202012 0.02199
NM_006261.5(PROP1):c.174G>A (p.Pro58=) rs2233784 0.02188
NM_006261.5(PROP1):c.*419C>T rs116225539 0.02154
NM_025000.4(DCAF17):c.*188T>A rs142315519 0.02083
NM_005149.3(TBX19):c.*469G>A rs16860362 0.01991
NM_000061.3(BTK):c.954T>C (p.Ser318=) rs5991926 0.01964
NM_005149.3(TBX19):c.917-14G>A rs71632355 0.01897
NM_025000.4(DCAF17):c.*3829G>A rs59827170 0.01646
NM_025000.4(DCAF17):c.*2183C>G rs73976170 0.01636
NM_025000.4(DCAF17):c.*1005A>G rs73976168 0.01517
NM_025000.4(DCAF17):c.*3712A>G rs74780004 0.01515
NM_005149.3(TBX19):c.*186G>A rs10918869 0.01378
NM_033343.4(LHX4):c.*97T>G rs145063714 0.01162
NM_002303.6(LEPR):c.2096C>T (p.Thr699Met) rs34499590 0.01048
NM_025000.4(DCAF17):c.*2348G>A rs112519318 0.01011
NM_021728.4(OTX2):c.459C>T (p.Ser153=) rs34537598 0.00961
NM_005149.3(TBX19):c.105C>T (p.Asp35=) rs34284181 0.00937
NM_021728.4(OTX2):c.97+12C>T rs28757218 0.00889
NM_033343.4(LHX4):c.*286G>C rs80203153 0.00865
NM_012414.4(RAB3GAP2):c.*1130A>G rs548918189 0.00800
NM_033343.4(LHX4):c.384C>T (p.Asp128=) rs141139762 0.00712
NM_033343.4(LHX4):c.*130C>T rs59623342 0.00680
NM_000306.4(POU1F1):c.666-5G>A rs76296626 0.00674
NM_033343.4(LHX4):c.*445G>T rs57069480 0.00607
NM_005149.3(TBX19):c.1122C>T (p.His374=) rs34885709 0.00575
NM_005149.3(TBX19):c.*544G>A rs144304383 0.00566
NM_005149.3(TBX19):c.761T>C (p.Val254Ala) rs77425733 0.00523
NM_178138.6(LHX3):c.*825C>A rs3739470 0.00510
NM_033343.4(LHX4):c.63T>C (p.Gly21=) rs75857235 0.00465
NM_025000.4(DCAF17):c.*1521A>G rs77176791 0.00434
NM_012414.4(RAB3GAP2):c.1779+7G>A rs111345353 0.00390
NM_000061.3(BTK):c.*221G>T rs1122765 0.00340
NM_012414.4(RAB3GAP2):c.3924G>C (p.Thr1308=) rs73098539 0.00338
NM_012414.4(RAB3GAP2):c.*925C>T rs185747953 0.00318
NM_000823.4(GHRHR):c.673G>A (p.Val225Ile) rs28371560 0.00225
NM_178138.6(LHX3):c.*185T>A rs144976921 0.00202
NM_005149.3(TBX19):c.-21G>A rs187423054 0.00201
NM_025000.4(DCAF17):c.127-15C>A rs146556466 0.00184
NM_025000.4(DCAF17):c.1320T>C (p.Ala440=) rs3731980 0.00143
NM_033343.4(LHX4):c.*119T>C rs180725260 0.00142
NM_025000.4(DCAF17):c.*1034G>A rs3731979 0.00114
NM_025000.4(DCAF17):c.*378T>C rs3795997 0.00114
NM_005149.3(TBX19):c.*1234C>T rs149712948 0.00066
NM_025000.4(DCAF17):c.*1965A>G rs569108215 0.00051
NM_021728.4(OTX2):c.*779G>A rs138197536 0.00041
NM_012414.4(RAB3GAP2):c.1709A>G (p.Asn570Ser) rs143286302 0.00006
NM_021728.4(OTX2):c.*966A>G rs57390094 0.00006
NM_033343.4(LHX4):c.1165C>A (p.Pro389Thr) rs145433128 0.00006
NM_012414.4(RAB3GAP2):c.*2043G>A rs367962640 0.00003
NM_012414.4(RAB3GAP2):c.2008C>G (p.Leu670Val) rs201613456 0.00002
NM_033343.4(LHX4):c.1160A>C (p.His387Pro) rs200187045 0.00001
NM_000230.3(LEP):c.*1720A>G rs10954174
NM_000230.3(LEP):c.*2410G>A rs28959474
NM_000306.4(POU1F1):c.*138T>A rs190287993
NM_000306.4(POU1F1):c.*213= rs6792500
NM_002303.6(LEPR):c.*346CA[8] rs10552268
NM_002303.6(LEPR):c.1968G>C (p.Lys656Asn) rs1805094
NM_005149.3(TBX19):c.*922GAAA[5] rs67726248
NM_005149.3(TBX19):c.603+10_603+11insTTGT rs72294615
NM_006261.5(PROP1):c.152G>C (p.Gly51Ala) rs2233783
NM_012414.4(RAB3GAP2):c.*2920CTT[1] rs3217443
NM_012414.4(RAB3GAP2):c.812-6del rs35396665
NM_017780.4(CHD7):c.*127del rs11322994
NM_025000.4(DCAF17):c.*1565del rs560178345
NM_025000.4(DCAF17):c.*2775G>T rs16859404
NM_033343.4(LHX4):c.*17C>A rs116482990

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