ClinVar Miner

Variants with conflicting interpretations studied for History of neurodevelopmental disorder

Coded as:
Minimum review status of the submission for History of neurodevelopmental disorder: Collection method of the submission for History of neurodevelopmental disorder:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
30 32 0 57 40 0 6 88

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All conditions
History of neurodevelopmental disorder pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 1 1 0 1
likely pathogenic 1 0 1 0 0
uncertain significance 1 2 0 18 11
likely benign 0 0 16 0 32
benign 0 1 1 23 0

Condition to condition summary #

Total conditions: 17
Download table as spreadsheet
Condition Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
not provided 0 42 0 34 27 0 4 61
not specified 0 28 0 31 18 0 1 48
Severe neonatal-onset encephalopathy with microcephaly; Syndromic X-linked intellectual disability Lubs type; X-linked intellectual disability-psychosis-macroorchidism syndrome; Rett syndrome; Autism, susceptibility to, X-linked 3 0 0 0 6 0 0 0 6
MECP2-related condition 0 4 0 5 0 0 0 5
CDKL5-related condition 0 2 0 2 0 0 0 2
Charcot-Marie-Tooth Neuropathy X 0 0 0 2 0 0 0 2
FANCB-related condition 0 0 0 0 2 0 0 2
KIF1A-related condition 0 0 0 1 1 0 0 2
Spastic paraplegia 0 0 0 0 2 0 0 2
Abnormal brain morphology 0 0 0 0 0 0 1 1
BCOR-related condition 0 1 0 1 0 0 0 1
FGD1-related condition 0 0 0 0 0 0 1 1
Intellectual disability-hypotonic facies syndrome, X-linked 0 0 0 1 0 0 0 1
L1CAM-related condition 0 0 0 0 1 0 0 1
RAI1-related condition 0 0 0 1 0 0 0 1
ZNF674-related condition 0 0 0 0 1 0 0 1
ZNF81-related condition 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 88
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001032382.2(PQBP1):c.180-3C>T rs741932 0.57792
NM_006950.3(SYN1):c.510T>C (p.Asn170=) rs1142636 0.39391
NM_005765.3(ATP6AP2):c.285G>A (p.Ser95=) rs34217273 0.01468
NM_006950.3(SYN1):c.1699A>G (p.Thr567Ala) rs200533370 0.01462
NM_001330078.2(NRXN1):c.4068G>A (p.Thr1356=) rs74714098 0.01437
NM_006950.3(SYN1):c.912C>T (p.Ala304=) rs62636605 0.01433
NM_001330078.2(NRXN1):c.3408G>A (p.Thr1136=) rs80094872 0.00737
NM_007137.5(ZNF81):c.129A>G (p.Arg43=) rs148626389 0.00663
NM_002764.4(PRPS1):c.456A>G (p.Leu152=) rs61735617 0.00632
NM_001244008.2(KIF1A):c.4604C>T (p.Ala1535Val) rs141441058 0.00470
NM_006306.4(SMC1A):c.*14C>T rs112727682 0.00436
NM_016032.4(ZDHHC9):c.975C>T (p.Ser325=) rs139619000 0.00414
NM_005634.3(SOX3):c.157G>C (p.Val53Leu) rs200361128 0.00403
NM_001190417.2(ZNF674):c.692A>G (p.Lys231Arg) rs201621696 0.00400
NM_001372044.2:c.1116C>T (p.Ser372=) rs201282170 0.00386
NM_001244008.2(KIF1A):c.3259C>T (p.Pro1087Ser) rs143037290 0.00369
NM_000266.4(NDP):c.*14G>A rs73475744 0.00365
NM_000330.4(RS1):c.184+3118C>T rs139155110 0.00352
NM_000330.4(RS1):c.184+3199G>A rs36022183 0.00345
NM_001018113.3(FANCB):c.1996G>A (p.Gly666Ser) rs145110602 0.00343
NM_001110792.2(MECP2):c.1225G>A (p.Glu409Lys) rs56268439 0.00308
NM_001324144.2(ZNF41):c.590A>G (p.Lys197Arg) rs148585367 0.00296
NM_001205019.2(GK):c.748-5A>T rs186543786 0.00284
NM_001123385.2(BCOR):c.408C>T (p.Ala136=) rs139802143 0.00258
NM_001110792.2(MECP2):c.1371G>A (p.Thr457=) rs3027927 0.00256
NM_005765.3(ATP6AP2):c.189C>T (p.Leu63=) rs150392503 0.00253
NM_002578.5(PAK3):c.531G>A (p.Glu177=) rs56270341 0.00239
NM_001323289.2(CDKL5):c.1332C>T (p.Arg444=) rs150844616 0.00210
NM_001110792.2(MECP2):c.933C>T (p.Thr311=) rs61748423 0.00200
NM_004840.3(ARHGEF6):c.169T>C (p.Cys57Arg) rs147131853 0.00200
NM_001363.5(DKC1):c.1456G>A (p.Gly486Arg) rs150319104 0.00192
NM_001330078.2(NRXN1):c.4473G>A (p.Ala1491=) rs113380721 0.00191
NM_001110792.2(MECP2):c.618C>T (p.Ser206=) rs61749711 0.00189
NM_001379110.1(SLC9A6):c.*8A>T rs200171451 0.00157
NM_020717.5(SHROOM4):c.1879C>T (p.Pro627Ser) rs150861758 0.00151
NM_001110792.2(MECP2):c.638C>T (p.Ala213Val) rs61748381 0.00150
NM_014271.4(IL1RAPL1):c.12G>A (p.Pro4=) rs143600441 0.00127
NM_004615.4(TSPAN7):c.515C>A (p.Pro172His) rs104894951 0.00126
NM_003179.3(SYP):c.877G>A (p.Gly293Ser) rs139475570 0.00122
NM_001110792.2(MECP2):c.246C>T (p.Ser82=) rs61754439 0.00119
NM_001018113.3(FANCB):c.1769T>C (p.Phe590Ser) rs142959373 0.00109
NM_001330078.2(NRXN1):c.4254A>G (p.Pro1418=) rs55923848 0.00109
NM_005333.5(HCCS):c.216G>C (p.Ala72=) rs144152239 0.00106
NM_001330078.2(NRXN1):c.4275G>T (p.Arg1425=) rs143495349 0.00096
NM_001330574.2(ZNF711):c.453A>C (p.Gly151=) rs139906124 0.00096
NM_001110792.2(MECP2):c.1233C>T (p.Pro411=) rs61753012 0.00081
NM_007325.5(GRIA3):c.397G>A (p.Ala133Thr) rs151086692 0.00081
NM_001110792.2(MECP2):c.*9G>A rs144008995 0.00080
NM_002764.4(PRPS1):c.447G>A (p.Pro149=) rs80338730 0.00068
NM_001244008.2(KIF1A):c.3494T>C (p.Ile1165Thr) rs35698242 0.00063
NM_000052.7(ATP7A):c.2070A>G (p.Glu690=) rs146692150 0.00060
NM_001110792.2(MECP2):c.411C>A (p.Ile137=) rs146107517 0.00059
NM_001324144.2(ZNF41):c.2114G>A (p.Arg705His) rs144904486 0.00050
NM_133433.4(NIPBL):c.8337G>A (p.Thr2779=) rs139108785 0.00047
NM_001330078.2(NRXN1):c.4392T>C (p.His1464=) rs112536447 0.00035
NM_001110792.2(MECP2):c.623C>G (p.Thr208Ser) rs61749713 0.00034
NM_001110792.2(MECP2):c.978C>T (p.Ile326=) rs61751446 0.00034
NM_001379110.1(SLC9A6):c.1083G>A (p.Leu361=) rs151178361 0.00022
NM_001244008.2(KIF1A):c.5155G>A (p.Val1719Met) rs200511467 0.00021
NM_001110792.2(MECP2):c.1173C>T (p.Pro391=) rs61752980 0.00020
NM_001110792.2(MECP2):c.429C>G (p.Ala143=) rs61748385 0.00018
NM_014141.6(CNTNAP2):c.1480G>A (p.Glu494Lys) rs149032771 0.00017
NM_001008537.3(NEXMIF):c.2951A>G (p.Asn984Ser) rs375623451 0.00013
NM_001110792.2(MECP2):c.789C>T (p.Pro263=) rs63582063 0.00013
NM_003611.3(OFD1):c.2060C>T (p.Pro687Leu) rs146251034 0.00013
NM_001244008.2(KIF1A):c.4955G>A (p.Arg1652Gln) rs376658420 0.00006
NM_001330078.2(NRXN1):c.4248G>A (p.Pro1416=) rs151195816 0.00006
NM_001278116.2(L1CAM):c.338G>A (p.Arg113His) rs781908326 0.00004
NM_001323289.2(CDKL5):c.93A>G (p.Arg31=) rs140332992 0.00004
NM_006517.5(SLC16A2):c.1117G>A (p.Val373Met) rs201039304 0.00004
NM_006950.3(SYN1):c.1321G>T (p.Ala441Ser) rs772106134 0.00004
NM_000381.4(MID1):c.250G>A (p.Asp84Asn) rs374851071 0.00002
NM_001110792.2(MECP2):c.727G>A (p.Gly243Arg) rs587783139 0.00002
NM_001123385.2(BCOR):c.780C>T (p.Ser260=) rs1430817668 0.00001
NM_005634.3(SOX3):c.753G>C (p.Pro251=) rs557384424 0.00001
NM_000033.4(ABCD1):c.838C>T (p.Arg280Cys) rs193922098
NM_000489.6(ATRX):c.6149T>C (p.Ile2050Thr) rs122445110
NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val)
NM_001110792.2(MECP2):c.379C>T (p.Arg127Cys) rs267608388
NM_001110792.2(MECP2):c.785G>A (p.Arg262His) rs61750227
NM_001123385.2(BCOR):c.1779C>A (p.Ser593=) rs17145652
NM_001271.4(CHD2):c.3735del (p.Lys1245fs) rs752940775
NM_004463.3(FGD1):c.1556G>A (p.Arg519His) rs398124157
NM_005120.3(MED12):c.6208CAG[9] (p.Gln2075_Gln2076dup) rs757160341
NM_006766.5(KAT6A):c.3353-4A>G rs762302738
NM_030665.4(RAI1):c.834GCA[9] (p.Gln288_Gln291del) rs371983878
NM_139058.3(ARX):c.441A>G (p.Ala147=) rs797045301
NM_176787.5(PIGN):c.1117-1= rs9959632

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