ClinVar Miner

Variants with conflicting interpretations studied for Global developmental delay

Coded as:
Minimum review status of the submission for Global developmental delay: Collection method of the submission for Global developmental 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
199 40 0 26 11 1 10 41

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
Global developmental delay pathogenic likely pathogenic uncertain significance likely benign benign protective other
pathogenic 0 15 4 1 1 1 1
likely pathogenic 11 0 2 0 0 0 0
uncertain significance 2 2 0 9 2 0 0
likely benign 1 1 1 0 1 1 1
benign 1 1 1 1 0 1 1

Condition to condition summary #

Total conditions: 63
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 39 0 22 8 1 7 31
POLG-related disorder 0 0 0 2 1 0 0 3
Marfanoid habitus and intellectual disability 0 0 0 2 0 0 1 2
Seizure; Focal-onset seizure; Irregular menstruation; Confusion; Palpitations; Periventricular heterotopia; Abnormal emotion 0 0 0 0 0 0 2 2
not specified 0 6 0 1 2 0 1 2
16p13.11 recurrent microdeletion syndrome 0 0 0 1 0 0 1 1
16p13.2-p13.13 microduplication syndrome 0 0 0 0 0 0 1 1
1p13.3 deletion syndrome 0 0 0 1 0 0 1 1
1q24q25 microdeletion syndrome 0 0 0 0 0 0 1 1
22q13.3 interstitial deletion 0 0 0 0 0 0 1 1
ATAD3 gene cluster related condition 0 0 0 0 1 0 1 1
Abnormal bleeding 0 0 0 1 0 0 1 1
Aminoaciduria 0 0 0 0 0 0 1 1
Anophthalmia-microphthalmia syndrome 0 0 0 1 0 0 1 1
Arthrogryphosis 0 0 0 0 1 0 1 1
Atypical behavior; Low-set ears; Prominent nasal bridge; Underdeveloped nasal alae; Intellectual disability, mild; Secondary microcephaly 0 0 0 0 1 0 1 1
Atypical behavior; Moderate global developmental delay 0 0 0 0 1 0 1 1
Autistic behavior; Absent speech 0 0 0 0 1 0 1 1
Autistic behavior; Moderate global developmental delay 0 0 0 1 0 0 1 1
Autistic behavior; Severe global developmental delay 0 0 0 1 0 0 1 1
CTNNB1-related disorders 0 0 0 1 0 0 0 1
DDC-related condition 0 0 0 0 1 0 0 1
Deep venous thrombosis 0 0 0 1 0 0 1 1
Delayed speech and language development 0 0 0 1 0 0 1 1
Epileptic encephalopathy 0 1 0 0 0 0 1 1
Focal-onset seizure 0 0 0 1 0 0 1 1
Gingival bleeding; Impaired epinephrine-induced platelet aggregation; Impaired collagen-induced platelet aggregation; Impaired arachidonic acid-induced platelet aggregation; Impaired ristocetin-induced platelet aggregation; Impaired thrombin-induced platelet aggregation; Impaired thromboxane A2 agonist-induced platelet aggregation 0 0 0 1 0 0 1 1
Global developmental delay 279 0 0 1 0 0 1 1
Global developmental delay; Expressive language delay; Secondary microcephaly 0 0 0 0 0 0 1 1
Global developmental delay; Seizure; Hypotelorism; Short philtrum; Infantile muscular hypotonia 0 0 0 0 1 0 1 1
Growth abnormality 0 0 0 0 1 0 1 1
Immunodeficiency 33; Ectodermal dysplasia and immunodeficiency 1; Incontinentia pigmenti syndrome; Immunodeficiency 47 0 0 0 0 0 0 1 1
Inherited Immunodeficiency Diseases 0 0 0 1 0 0 1 1
Intellectual disability, mild 0 0 0 0 1 0 1 1
Intellectual disability, severe 0 0 0 0 0 0 1 1
Internal malformations 0 0 0 0 1 0 1 1
Interstitial 6q microdeletion syndrome 0 0 0 0 0 0 1 1
KCNN2-related condition 0 0 0 1 0 0 0 1
LETM1-associated clinical spectrum with predominant nervous system involvement 0 0 0 0 0 0 1 1
LRP2-related condition 0 0 0 0 1 0 0 1
MBD5 associated neurodevelopmental disorder 0 0 0 0 0 0 1 1
MKS1-related condition 0 0 0 1 0 0 1 1
Muscle dystrophy 0 0 0 1 0 0 1 1
Neurodevelopmental abnormality 0 1 0 0 1 0 0 1
Neurodevelopmental delay 0 4 0 1 0 0 0 1
PPFIA3-related disorder 0 0 0 1 0 0 1 1
Pediatric metastatic thyroid tumour 0 0 0 1 0 0 1 1
Primary amenorrhea 0 0 0 1 1 0 1 1
RAPSN-Related Disorders 0 0 0 1 0 0 0 1
RHD DEL 0 0 0 0 0 0 1 1
Renal transitional cell carcinoma 0 0 0 1 0 0 1 1
SLC4A10-related neurodevelopmental disorder 0 0 0 1 0 0 1 1
SUCLA2-related condition 0 0 0 0 1 0 0 1
See cases 0 5 0 1 1 0 1 1
Seizure 0 0 0 1 1 0 1 1
Seizure; Hypotonia; Neurodevelopmental Disability 0 0 0 1 0 0 0 1
Silver Russell Syndrome-related disorder 0 0 0 0 1 0 1 1
Spastic paraplegia 0 0 0 1 1 0 1 1
Spinocerebellar ataxia, X-linked 0 0 0 0 0 1 0 1
Splenomegaly; Decreased circulating antibody level 0 0 0 0 0 0 1 1
TAX1BP3-related arrhythmogenic right ventricular cardiomyopathy 0 0 0 1 0 0 1 1
ZMYND11-related condition 0 0 0 1 0 0 0 1
ZNF331 deletion 0 0 0 0 1 0 1 1

All variants with conflicting interpretations #

Total variants: 41
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HGVS dbSNP gnomAD frequency
NM_020361.5(CPA6):c.799G>A (p.Gly267Arg) rs61738009 0.00239
NM_002693.3(POLG):c.1837C>T (p.His613Tyr) rs147407423 0.00166
NM_002693.3(POLG):c.1760C>T (p.Pro587Leu) rs113994096 0.00160
NM_002693.3(POLG):c.752C>T (p.Thr251Ile) rs113994094 0.00159
NM_004525.3(LRP2):c.13921A>T (p.Thr4641Ser) rs79179577 0.00123
NM_020361.5(CPA6):c.619C>G (p.Gln207Glu) rs35993949 0.00121
NM_032730.5(RTN4IP1):c.5A>C (p.Glu2Ala) rs138612238 0.00110
NM_003850.3(SUCLA2):c.236C>T (p.Ser79Leu) rs142289138 0.00062
NM_020987.5(ANK3):c.11678G>C (p.Ser3893Thr) rs12260663 0.00044
NM_006031.6(PCNT):c.644G>A (p.Cys215Tyr) rs138962786 0.00041
NM_001082971.2(DDC):c.1435A>G (p.Arg479Gly) rs200450773 0.00016
NM_005055.5(RAPSN):c.848T>C (p.Leu283Pro) rs104894293 0.00004
NM_020247.5(COQ8A):c.1228C>T (p.Arg410Ter) rs753254213 0.00004
NM_012123.4(MTO1):c.1282G>A (p.Ala428Thr) rs143747297 0.00003
NM_001543.5(NDST1):c.1831G>A (p.Gly611Ser) rs606231459 0.00001
NM_031407.7(HUWE1):c.9802C>T (p.Pro3268Ser) rs1045935059 0.00001
NM_057175.5(NAA15):c.239_240del (p.His80fs) rs779009256 0.00001
NM_000142.5(FGFR3):c.188C>T (p.Pro63Leu) rs371729802
NM_000314.8(PTEN):c.885_886del (p.Leu295_Cys296insTer) rs1564568350
NM_001083962.2(TCF4):c.1732C>T (p.Arg578Cys) rs2144406630
NM_001256012.3(MYH10):c.5681G>A (p.Arg1894Gln) rs1038557470
NM_001282531.3(ADNP):c.673C>T (p.Arg225Ter) rs1057518991
NM_001370100.5(ZMYND11):c.1798C>T (p.Arg600Trp) rs797044854
NM_001904.4(CTNNB1):c.1981C>T (p.Arg661Ter) rs748294403
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_003011.4(SET):c.130_133del (p.Arg44fs) rs1554776342
NM_003042.4(SLC6A1):c.1648G>A (p.Gly550Arg) rs886042046
NM_003076.5(SMARCD1):c.494G>A (p.Arg165Gln)
NM_003718.5(CDK13):c.2525A>G (p.Asn842Ser) rs878853160
NM_004333.6(BRAF):c.755G>C (p.Arg252Pro) rs1325951163
NM_004415.4(DSP):c.1783C>T (p.Gln595Ter)
NM_006087.4(TUBB4A):c.1228G>A (p.Glu410Lys) rs587777428
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys)
NM_006908.5(RAC1):c.116A>G (p.Asn39Ser)
NM_007144.3(PCGF2):c.194C>T (p.Pro65Leu)
NM_012318.3(LETM1):c.2220G>C (p.Ter740Tyr) rs2108832865
NM_013275.6(ANKRD11):c.1381_1384del (p.Glu461fs) rs1597464953
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_021614.4(KCNN2):c.1598_1600del (p.Leu533del) rs1554086554
NM_138967.4(SCAMP5):c.538G>T (p.Gly180Trp) rs1184981709
Single allele

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