ClinVar Miner

List of variants reported as benign for Pitt-Hopkins-like syndrome

Included ClinVar conditions (5):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 141
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HGVS dbSNP gnomAD frequency
NM_014141.6(CNTNAP2):c.*4797G>C rs2717829 0.82590
NM_001330078.2(NRXN1):c.4129-30181T>C rs9636391 0.82006
NM_014141.6(CNTNAP2):c.*279C>A rs987456 0.71838
NM_014141.6(CNTNAP2):c.3723G>A (p.Ala1241=) rs9648691 0.57506
NM_014141.5(CNTNAP2):c.-115G>A rs2462603 0.49254
NM_014141.6(CNTNAP2):c.*2157A>G rs1062072 0.48864
NM_014141.6(CNTNAP2):c.*3742A>G rs2530311 0.47166
NM_014141.6(CNTNAP2):c.1897+25A>G rs2074715 0.46942
NM_014141.6(CNTNAP2):c.551-11_551-10insG rs35167289 0.42413
NM_014141.6(CNTNAP2):c.3381+17A>C rs3779032 0.39925
NM_014141.6(CNTNAP2):c.*1557A>C rs3194 0.35771
NM_014141.6(CNTNAP2):c.*4934C>T rs2530310 0.34059
NM_014141.6(CNTNAP2):c.*1187G>A rs2530312 0.33729
NM_001330078.2(NRXN1):c.3364+20T>C rs3213756 0.25608
NM_001330078.2(NRXN1):c.-281T>C rs35228545 0.23029
NM_014141.6(CNTNAP2):c.*2921C>T rs10243309 0.22898
NM_001330078.2(NRXN1):c.-421A>C rs67661616 0.22388
NM_014141.6(CNTNAP2):c.2280A>G (p.Ser760=) rs10240503 0.22240
NM_014141.6(CNTNAP2):c.1777+10A>G rs2286127 0.20355
NM_001330078.2(NRXN1):c.*1911G>T rs11885824 0.20346
NM_014141.6(CNTNAP2):c.3248-4A>G rs3779031 0.18203
NM_014141.6(CNTNAP2):c.1659G>A (p.Ala553=) rs34592169 0.17471
NM_001330078.2(NRXN1):c.511C>T (p.Leu171=) rs1045874 0.17452
NM_001330078.2(NRXN1):c.-951T>C rs2287235 0.17294
NM_014141.6(CNTNAP2):c.*4738C>G rs10251347 0.15342
NM_001330078.2(NRXN1):c.*110G>A rs1045881 0.14719
NM_001330078.2(NRXN1):c.*1327C>G rs12998798 0.14393
NM_014141.6(CNTNAP2):c.*4839G>A rs10280038 0.11146
NM_014141.6(CNTNAP2):c.*3144A>G rs17170999 0.11137
NM_014141.6(CNTNAP2):c.*3928C>T rs73473919 0.11111
NM_014141.6(CNTNAP2):c.2256-6A>T rs10240482 0.10641
NM_014141.6(CNTNAP2):c.*1059A>T rs1062071 0.09994
NM_001330078.2(NRXN1):c.-563G>C rs62143025 0.07837
NM_001330078.2(NRXN1):c.-602G>A rs62143026 0.07832
NM_014141.6(CNTNAP2):c.2099-15T>C rs75858942 0.04429
NM_014141.6(CNTNAP2):c.*3531G>A rs79360609 0.04371
NM_014141.6(CNTNAP2):c.1710G>A (p.Ser570=) rs2286128 0.03626
NM_001330078.2(NRXN1):c.-883T>C rs10188340 0.03596
NM_014141.6(CNTNAP2):c.*3392C>T rs115420302 0.02775
NM_014141.6(CNTNAP2):c.3476-15C>A rs77706740 0.02606
NC_000007.14:g.146116001A>G rs34712024 0.02519
NM_014141.6(CNTNAP2):c.*1017T>G rs77001133 0.02487
NM_014141.6(CNTNAP2):c.*5022C>T rs17171006 0.02086
NM_014141.6(CNTNAP2):c.3797-6C>T rs79777576 0.01899
NM_001330078.2(NRXN1):c.900C>T (p.Pro300=) rs2303298 0.01844
NM_014141.6(CNTNAP2):c.318C>T (p.Ser106=) rs61732853 0.01773
NM_001330078.2(NRXN1):c.*1692T>C rs77838429 0.01480
NM_001330078.2(NRXN1):c.4068G>A (p.Thr1356=) rs74714098 0.01437
NM_014141.6(CNTNAP2):c.*678G>C rs2717809 0.01414
NM_014141.6(CNTNAP2):c.*1433A>G rs78484397 0.01362
NM_001330078.2(NRXN1):c.*1539C>G rs112108943 0.01263
NM_001330078.2(NRXN1):c.*2511G>C rs148938313 0.01190
NM_001330078.2(NRXN1):c.*2878G>A rs146778534 0.01088
NM_014141.6(CNTNAP2):c.1854C>T (p.Gly618=) rs61732849 0.01075
NM_001330078.2(NRXN1):c.*1365A>G rs147121881 0.01048
NM_014141.6(CNTNAP2):c.1119G>A (p.Thr373=) rs73471053 0.00970
NM_001330078.2(NRXN1):c.4217-16A>C rs74520052 0.00964
NM_014141.6(CNTNAP2):c.834T>C (p.Ser278=) rs61732854 0.00910
NM_001330078.2(NRXN1):c.772+1140G>A rs61658382 0.00837
NM_014141.6(CNTNAP2):c.1308C>T (p.Asn436=) rs79039458 0.00749
NM_001330078.2(NRXN1):c.3408G>A (p.Thr1136=) rs80094872 0.00737
NM_014141.6(CNTNAP2):c.*2670T>G rs116187496 0.00661
NM_014141.6(CNTNAP2):c.3633G>A (p.Glu1211=) rs138477292 0.00609
NM_001330078.2(NRXN1):c.*2372G>A rs116370948 0.00580
NM_001330078.2(NRXN1):c.3249C>T (p.Pro1083=) rs116236999 0.00578
NM_014141.6(CNTNAP2):c.1247C>T (p.Ala416Val) rs34456867 0.00548
NM_001330078.2(NRXN1):c.2421C>T (p.Asn807=) rs115211871 0.00535
NM_001330078.2(NRXN1):c.2143+19A>G rs150513096 0.00534
NM_001330078.2(NRXN1):c.3933A>G (p.Ala1311=) rs79970751 0.00503
NM_001330078.2(NRXN1):c.1760-16C>T rs79422704 0.00472
NM_014141.6(CNTNAP2):c.1137C>T (p.Asn379=) rs78543192 0.00454
NM_014141.6(CNTNAP2):c.3382-7C>T rs189589051 0.00454
NM_014141.6(CNTNAP2):c.3675G>A (p.Ser1225=) rs142331907 0.00417
NM_001330078.2(NRXN1):c.*540T>A rs74421750 0.00411
NM_014141.6(CNTNAP2):c.854G>C (p.Gly285Ala) rs150918383 0.00405
NM_014141.6(CNTNAP2):c.1311C>T (p.Ile437=) rs56356283 0.00340
NM_014141.6(CNTNAP2):c.2892G>A (p.Ser964=) rs148104020 0.00330
NM_001330078.2(NRXN1):c.1285C>T (p.Pro429Ser) rs78540316 0.00323
NM_014141.6(CNTNAP2):c.3585G>A (p.Arg1195=) rs77789547 0.00300
NM_014141.6(CNTNAP2):c.1083G>A (p.Val361=) rs139180845 0.00269
NM_014141.6(CNTNAP2):c.3105C>T (p.Asn1035=) rs112483670 0.00264
NM_014141.6(CNTNAP2):c.1220A>G (p.Asn407Ser) rs143877693 0.00253
NM_014141.6(CNTNAP2):c.551-15_551-14insG rs201428458 0.00247
NM_014141.6(CNTNAP2):c.681C>T (p.His227=) rs142984073 0.00236
NM_014141.6(CNTNAP2):c.551-11T>G rs78223661 0.00210
NM_001330078.2(NRXN1):c.4473G>A (p.Ala1491=) rs113380721 0.00191
NM_001330078.2(NRXN1):c.2385C>G (p.Pro795=) rs147984237 0.00166
NM_001330078.2(NRXN1):c.1575A>G (p.Arg525=) rs201941844 0.00155
NM_001330078.2(NRXN1):c.501C>G (p.Leu167=) rs200248561 0.00145
NM_001330078.2(NRXN1):c.222C>T (p.Gly74=) rs201592993 0.00135
NM_014141.6(CNTNAP2):c.3247+16C>T rs370512570 0.00124
NM_014141.6(CNTNAP2):c.-49T>G rs549396215 0.00123
NM_001330078.2(NRXN1):c.3045C>T (p.Ala1015=) rs56402642 0.00109
NM_014141.6(CNTNAP2):c.3011-11C>T rs201397443 0.00097
NM_001330078.2(NRXN1):c.4275G>T (p.Arg1425=) rs143495349 0.00096
NM_001330078.2(NRXN1):c.2772C>T (p.Tyr924=) rs200182626 0.00083
NM_014141.6(CNTNAP2):c.2205C>A (p.Asn735Lys) rs200610099 0.00071
NM_001330078.2(NRXN1):c.1945A>G (p.Ile649Val) rs200074974 0.00062
NM_001330078.2(NRXN1):c.105C>A (p.Gly35=) rs55640811 0.00059
NM_001330078.2(NRXN1):c.2605C>A (p.Leu869Met) rs201818223 0.00044
NM_014141.6(CNTNAP2):c.2190C>T (p.Cys730=) rs74354654 0.00029
NM_014141.6(CNTNAP2):c.2895C>A (p.Gly965=) rs75688908 0.00028
NM_001330078.2(NRXN1):c.2347+18C>A rs150460414 0.00016
NM_001330078.2(NRXN1):c.821-4A>G rs768708962 0.00009
NM_001330078.2(NRXN1):c.1833T>C (p.Asp611=) rs190377845 0.00006
NM_001330078.2(NRXN1):c.2730G>A (p.Lys910=) rs192909520 0.00006
NM_001330078.2(NRXN1):c.2313A>G (p.Leu771=) rs779330397 0.00005
NM_001330078.2(NRXN1):c.3219C>T (p.Asn1073=) rs563089155 0.00005
NM_014141.6(CNTNAP2):c.3716-6C>G rs77025884 0.00004
NM_001330078.2(NRXN1):c.3403A>G (p.Ile1135Val) rs765360600 0.00003
NM_001330078.2(NRXN1):c.600C>T (p.Gly200=) rs201481698 0.00003
NM_014141.6(CNTNAP2):c.1998C>T (p.Ser666=) rs759797092 0.00003
NM_001330078.2(NRXN1):c.1326A>C (p.Val442=) rs201485014 0.00001
NM_014141.6(CNTNAP2):c.402+13C>A rs532060379 0.00001
NM_001330078.2(NRXN1):c.*2105A>C rs112364713
NM_001330078.2(NRXN1):c.*967_*970dup rs3839058
NM_001330078.2(NRXN1):c.1135-13dup
NM_001330078.2(NRXN1):c.1760-11C>G rs199550097
NM_001330078.2(NRXN1):c.1843C>T (p.Leu615=) rs201029409
NM_001330078.2(NRXN1):c.2348-13C>A
NM_001330078.2(NRXN1):c.3547-14dup
NM_001330078.2(NRXN1):c.3547-18dup rs749772679
NM_001330078.2(NRXN1):c.4216+17T>A rs200836763
NM_001330078.2(NRXN1):c.4216+17del rs2104381080
NM_014141.6(CNTNAP2):c.*1175TCTT[1] rs72035437
NM_014141.6(CNTNAP2):c.*175dup rs61125105
NM_014141.6(CNTNAP2):c.*2935_*2936del rs544152145
NM_014141.6(CNTNAP2):c.*3999dup rs35835723
NM_014141.6(CNTNAP2):c.*600CTGA[3] rs3058181
NM_014141.6(CNTNAP2):c.*916TAGTT[1] rs569195865
NM_014141.6(CNTNAP2):c.1566G>A (p.Gln522=) rs535454043
NM_014141.6(CNTNAP2):c.2356G>T (p.Val786Leu) rs138517537
NM_014141.6(CNTNAP2):c.2773+76del rs5888307
NM_014141.6(CNTNAP2):c.3476-9_3476-8del
NM_014141.6(CNTNAP2):c.3678C>T (p.Ser1226=) rs201219937
NM_014141.6(CNTNAP2):c.3716-17TCTT[3] rs142426153
NM_014141.6(CNTNAP2):c.3716-5_3716-4insGT rs60451214
NM_014141.6(CNTNAP2):c.3716-7_3716-6insTT rs72268642
NM_014141.6(CNTNAP2):c.551-8del rs370377093
NM_014141.6(CNTNAP2):c.551-8dup rs370377093
NM_014141.6(CNTNAP2):c.98-19_98-16del rs796052367

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