ClinVar Miner

Variants with conflicting interpretations studied for Neurodevelopmental delay

Coded as:
Minimum review status of the submission for Neurodevelopmental delay: Collection method of the submission for Neurodevelopmental delay:
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
200 48 0 33 4 0 15 49

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
Neurodevelopmental delay pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 19 4 0 0
likely pathogenic 14 0 9 1 0
uncertain significance 0 1 0 3 2

Condition to condition summary #

Total conditions: 19
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 56 0 22 4 0 12 36
not specified 0 3 0 1 0 0 5 6
ACTA1-related myopathies 0 0 0 1 0 0 0 1
CYB5R3-related disorder 0 0 0 0 1 0 0 1
Cardiovascular phenotype 0 2 0 0 0 0 1 1
Epilepsy, childhood absence, susceptibility to, 1; Epilepsy, childhood absence, susceptibility to, 5 0 0 0 1 0 0 0 1
Epilepsy, childhood absence, susceptibility to, 5 0 0 0 1 0 0 0 1
Epileptic encephalopathy 0 0 0 1 0 0 0 1
Global developmental delay 0 4 0 1 0 0 0 1
Global developmental delay; Seizure 0 0 0 1 0 0 0 1
HCN2 related developmental and epileptic encephalopathy 0 0 0 1 0 0 0 1
NSD2-related disorder 0 0 0 1 0 0 0 1
ROBO1-related disorder 0 0 0 0 1 0 0 1
SPATA5L1-associated disorder 0 0 0 1 0 0 0 1
See cases 0 8 0 1 0 0 0 1
Seizure 0 1 0 1 0 0 0 1
Seizure; Hypotonia; Neurodevelopmental Disability 0 0 0 1 0 0 0 1
UNC80-related disorder 0 0 0 0 0 0 1 1
recessive ARS-related multisystem disease 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 49
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_002941.4(ROBO1):c.2204G>A (p.Ser735Asn) rs34515208 0.00193
NM_001371986.1(UNC80):c.1806G>C (p.Gln602His) rs200473652 0.00163
NM_000398.7(CYB5R3):c.890G>A (p.Arg297His) rs76458556 0.00145
NM_024063.3(AFG2B):c.527G>T (p.Gly176Val) rs145451123 0.00098
NM_001371986.1(UNC80):c.4544C>T (p.Ala1515Val) rs750442854 0.00003
NM_001673.5(ASNS):c.146G>A (p.Arg49Gln) rs769236847 0.00003
NM_032043.3(BRIP1):c.2543G>A (p.Arg848His) rs374334794 0.00003
NM_001110556.2(FLNA):c.1966C>T (p.Leu656Phe) rs137853311 0.00002
NM_001374828.1(ARID1B):c.5902C>T (p.Arg1968Cys) rs766931727 0.00001
NM_001378969.1(KCND3):c.1645C>T (p.Arg549Cys) rs1294150954 0.00001
NM_003680.4(YARS1):c.176T>C (p.Ile59Thr) rs774466323 0.00001
NM_015937.6(PIGT):c.1079G>T (p.Gly360Val) rs1277383877 0.00001
NM_018297.4(NGLY1):c.931G>A (p.Glu311Lys) rs201791209 0.00001
NM_024063.3(AFG2B):c.2087G>T (p.Cys696Phe) rs747249958 0.00001
NM_000188.3(HK1):c.1240G>A (p.Gly414Arg) rs2132871580
NM_000276.4(OCRL):c.940-11G>A rs776743373
NM_000314.8(PTEN):c.94ATT[1] (p.Ile33del) rs1554893765
NM_000474.4(TWIST1):c.309C>G (p.Tyr103Ter) rs104894054
NM_000814.6(GABRB3):c.358G>A (p.Asp120Asn) rs886037938
NM_000814.6(GABRB3):c.901C>T (p.Pro301Ser) rs1889966666
NM_001100.4(ACTA1):c.809G>A (p.Gly270Asp) rs1553255362
NM_001110556.2(FLNA):c.134A>G (p.Gln45Arg) rs398123613
NM_001110792.2(MECP2):c.1198_1208del (p.Pro399_Pro400insTer) rs2065919863
NM_001110792.2(MECP2):c.1240_1241insT (p.Pro414fs) rs2148659573
NM_001110792.2(MECP2):c.433C>T (p.Arg145Cys) rs28934904
NM_001127222.2(CACNA1A):c.4988G>A (p.Arg1663Gln) rs121908247
NM_001194.4(HCN2):c.1432_1434del (p.Glu478del) rs2144522815
NM_001330288.2(SMARCC2):c.326dup (p.Tyr109Ter) rs2135750656
NM_001348323.3(TRIP12):c.4302_4303del (p.Tyr1435fs) rs2154259932
NM_001348716.2(KDM6B):c.1483C>T (p.Arg495Ter) rs1597842212
NM_001353345.2(SETD1B):c.5375G>A (p.Arg1792Gln) rs2137588997
NM_001376.5(DYNC1H1):c.791G>A (p.Arg264Gln) rs713993043
NM_001378969.1(KCND3):c.1111G>A (p.Gly371Arg) rs1057521793
NM_001429.4(EP300):c.104_107del (p.Ser35fs) rs886037664
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg) rs1131691302
NM_003660.4(PPFIA3):c.2717C>T (p.Ser906Leu) rs2513986316
NM_004493.3(HSD17B10):c.439C>T (p.Arg147Cys) rs1064794694
NM_004975.4(KCNB1):c.968C>T (p.Thr323Ile) rs1569017257
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys) rs863225082
NM_006908.5(RAC1):c.116A>G (p.Asn39Ser) rs1554263624
NM_006940.6(SOX5):c.1678A>G (p.Met560Val) rs1591908609
NM_007347.5(AP4E1):c.1694C>T (p.Ala565Val) rs142762839
NM_014991.6(WDFY3):c.8467C>T (p.Arg2823Trp) rs1131692269
NM_014991.6(WDFY3):c.8864_8867dup (p.Phe2957fs) rs878853167
NM_016604.4(KDM3B):c.4414C>T (p.Arg1472Ter) rs1561796122
NM_133330.3(NSD2):c.1676_1679del rs1553873247
NM_145239.3(PRRT2):c.649dup (p.Arg217fs) rs587778771
NM_177559.3(CSNK2A1):c.593A>G (p.Lys198Arg) rs869312840

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