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

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Minimum conflict level: Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)
		ClinVar version:

Total variants: 89

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HGVS	dbSNP	gnomAD frequency
NM_000230.3(LEP):c.-39G>A	rs2167270	0.37538
NM_000439.5(PCSK1):c.*1041T>A	rs17085675	0.31161
NM_000439.5(PCSK1):c.*1530T>C	rs2882298	0.30559
NM_000439.5(PCSK1):c.1993C>G (p.Gln665Glu)	rs6234	0.23916
NM_002303.6(LEPR):c.1029T>C (p.Ser343=)	rs1805134	0.23693
NM_017780.3(CHD7):c.*2104T>A	rs16926520	0.11399
NM_000230.3(LEP):c.*2205G>A	rs41457646	0.10795
NM_000230.3(LEP):c.*400G>T	rs17151922	0.09344
NM_000406.2(GNRHR):c.-731C>T	rs2630490	0.09029
NM_000406.2(GNRHR):c.-62G>A	rs2627261	0.09015
NM_000406.2(GNRHR):c.-1570C>G	rs28643407	0.08726
NM_003865.3(HESX1):c.374A>G (p.Asn125Ser)	rs9878928	0.07568
NM_000406.3(GNRHR):c.*2441T>C	rs2319657	0.06538
NM_000439.5(PCSK1):c.612C>T (p.Asn204=)	rs6231	0.04494
NM_000823.4(GHRHR):c.*147A>C	rs2586	0.04030
NM_000230.3(LEP):c.*1243A>G	rs6966536	0.02955
NM_000823.4(GHRHR):c.*236C>A	rs28371564	0.02852
NM_000230.3(LEP):c.280G>A (p.Val94Met)	rs17151919	0.02565
NM_002303.6(LEPR):c.2597+15G>C	rs6693573	0.01870
NM_000406.3(GNRHR):c.*2767T>C	rs12507392	0.01831
NM_002303.6(LEPR):c.3024A>G (p.Ser1008=)	rs6413506	0.01632
NM_002303.6(LEPR):c.*232G>A	rs116819844	0.01407
NM_178138.6(LHX3):c.454+3C>T	rs34356735	0.01349
NM_178138.6(LHX3):c.108G>A (p.Gln36=)	rs33998096	0.01071
NM_000406.2(GNRHR):c.-541G>A	rs140006155	0.00890
NM_000406.3(GNRHR):c.144C>G (p.Leu48=)	rs35400155	0.00800
NM_178138.6(LHX3):c.*747C>G	rs146752425	0.00714
NM_002303.6(LEPR):c.2958C>T (p.Tyr986=)	rs1805095	0.00643
NM_017526.5(LEPROT):c.21C>T (p.Leu7=)	rs13306523	0.00623
NM_000061.3(BTK):c.141+11C>T	rs138411530	0.00620
NM_012414.4(RAB3GAP2):c.*2327A>G	rs139079455	0.00513
NM_012414.4(RAB3GAP2):c.961-14G>T	rs148886986	0.00475
NM_012414.4(RAB3GAP2):c.*2638C>T	rs74139286	0.00455
NM_012414.4(RAB3GAP2):c.*2464T>C	rs111341601	0.00444
NM_025000.4(DCAF17):c.*677C>A	rs115798465	0.00417
NM_000406.3(GNRHR):c.*385A>G	rs111894416	0.00401
NM_012414.4(RAB3GAP2):c.*2399A>G	rs115637988	0.00369
NM_012414.4(RAB3GAP2):c.*1404T>C	rs188666578	0.00355
NM_005149.3(TBX19):c.*267A>G	rs146307337	0.00347
NM_012414.4(RAB3GAP2):c.*1271C>T	rs193019999	0.00318
NM_025000.4(DCAF17):c.*530A>G	rs115676571	0.00277
NM_012414.4(RAB3GAP2):c.*1527G>C	rs185153185	0.00255
NM_012414.4(RAB3GAP2):c.3966A>G (p.Lys1322=)	rs150226729	0.00206
NM_012414.4(RAB3GAP2):c.4060A>G (p.Ile1354Val)	rs59190330	0.00174
NM_033343.4(LHX4):c.924T>C (p.Tyr308=)	rs146655496	0.00159
NM_012414.4(RAB3GAP2):c.*645C>T	rs188031183	0.00158
NM_012414.4(RAB3GAP2):c.39C>T (p.Asp13=)	rs145667920	0.00149
NM_000061.3(BTK):c.615G>T (p.Glu205Asp)	rs35877704	0.00114
NM_178138.6(LHX3):c.*791G>A	rs12237402	0.00091
NM_178138.6(LHX3):c.920G>C (p.Arg307Pro)	rs182345541	0.00073
NM_003865.3(HESX1):c.385G>A (p.Val129Ile)	rs143057250	0.00064
NM_012414.4(RAB3GAP2):c.3991C>A (p.Leu1331Ile)	rs149842844	0.00050
NM_025000.4(DCAF17):c.*2591A>G	rs748228250	0.00043
NM_025000.4(DCAF17):c.*2429A>G	rs778932293	0.00041
NM_012414.4(RAB3GAP2):c.2807-15G>A	rs200407685	0.00038
NM_033343.4(LHX4):c.90C>T (p.Cys30=)	rs147491286	0.00030
NM_033343.4(LHX4):c.37G>A (p.Val13Ile)	rs146664099	0.00026
NM_025000.4(DCAF17):c.*15T>C	rs146258833	0.00024
NM_000823.4(GHRHR):c.272C>T (p.Ala91Val)	rs144372265	0.00019
NM_033343.4(LHX4):c.849A>C (p.Gly283=)	rs373879455	0.00016
NM_021728.4(OTX2):c.*316G>A	rs142727455	0.00015
NM_012414.4(RAB3GAP2):c.2304G>A (p.Leu768=)	rs140146408	0.00014
NM_012414.4(RAB3GAP2):c.3143A>G (p.His1048Arg)	rs151244742	0.00013
NM_021728.4(OTX2):c.641C>A (p.Thr214Asn)	rs150982073	0.00013
NM_000061.3(BTK):c.895-10G>A	rs370812397	0.00010
NM_025000.4(DCAF17):c.579C>A (p.Phe193Leu)	rs150095386	0.00008
NM_033343.4(LHX4):c.774C>T (p.Phe258=)	rs565803862	0.00007
NM_033343.4(LHX4):c.398T>C (p.Met133Thr)	rs371899398	0.00006
NM_021728.4(OTX2):c.840T>C (p.Ala280=)	rs201396096	0.00005
NM_033343.4(LHX4):c.223G>A (p.Val75Ile)	rs749318884	0.00004
NM_000823.4(GHRHR):c.151A>G (p.Thr51Ala)	rs141571344	0.00003
NM_025000.4(DCAF17):c.*3705A>G	rs577520268	0.00003
NM_178138.6(LHX3):c.79+1814G>T	rs569646536	0.00003
NM_005149.3(TBX19):c.*1266C>T	rs544283210	0.00001
NM_012414.4(RAB3GAP2):c.*572G>T	rs540128548	0.00001
NM_000061.3(BTK):c.*334TG[4]	rs200445244
NM_000230.3(LEP):c.*2595C>A	rs28959475
NM_000230.3(LEP):c.2820_2822dup	rs56247456
NM_000439.5(PCSK1):c.737_739dup	rs5869716
NM_000439.5(PCSK1):c.*826del	rs34572181
NM_000515.4(GH1):c.-68A>G	rs6171
NM_000515.5(GH1):c.-63A>C	rs695
NM_000515.5(GH1):c.-63A>T	rs695
NM_002303.6(LEPR):c.60_61insCTTTA	rs75054066
NM_005149.3(TBX19):c.603+10_603+11insTT	rs373712384
NM_012414.4(RAB3GAP2):c.1694_1695insACA	rs143194915
NM_012414.4(RAB3GAP2):c.*2512dup	rs143756119
NM_012414.4(RAB3GAP2):c.304+12A>G	rs530311696
NM_033343.4(LHX4):c.*26C>T	rs138054044

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