ClinVar Miner

Variants with conflicting interpretations studied for Abnormality of brain morphology

Coded as:
Minimum review status of the submission for Abnormality of brain morphology: Y axis collection method of the submission for Abnormality of brain morphology:
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 Variants with at least 2 submissions 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 kind of conflict
62 0 0 13 0 0 15 28

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
Abnormality of brain morphology pathogenic uncertain significance likely benign benign
likely pathogenic 13 10 4 7

Condition to condition summary #

Total conditions: 24
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
not provided 0 2 0 2 0 0 6 8
not specified 0 0 0 0 0 0 7 7
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies 0 0 0 4 0 0 0 4
Galactosylceramide beta-galactosidase deficiency 0 0 0 0 0 0 2 2
History of neurodevelopmental disorder 0 0 0 0 0 0 2 2
NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND CORTICAL ATROPHY 0 0 0 2 0 0 0 2
Cerebellar ataxia 0 0 0 0 0 0 1 1
Combined oxidative phosphorylation deficiency 7 0 0 0 1 0 0 0 1
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 63 0 0 0 1 0 0 0 1
Early Infantile Epileptic Encephalopathy, Autosomal Dominant 0 0 0 0 0 0 1 1
Early infantile epileptic encephalopathy 0 0 0 0 0 0 1 1
Emery-Dreifuss muscular dystrophy 0 0 0 0 0 0 1 1
Inborn genetic diseases 0 0 0 0 0 0 1 1
Infantile neuroaxonal dystrophy 0 0 0 0 0 0 1 1
Mental retardation, X-linked 1 0 0 0 0 0 0 1 1
Multiple congenital anomalies-hypotonia-seizures syndrome 1 0 0 0 1 0 0 0 1
Non-ketotic hyperglycinemia 0 0 0 0 0 0 1 1
Primary autosomal recessive microcephaly 1 0 0 0 1 0 0 0 1
Seizures 0 0 0 0 0 0 1 1
Smith-Lemli-Opitz syndrome 0 0 0 1 0 0 0 1
Spastic paraplegia 0 0 0 0 0 0 1 1
Spastic paraplegia 11, autosomal recessive 0 0 0 1 0 0 0 1
Spastic paraplegia 55, autosomal recessive 0 0 0 1 0 0 0 1
Spinocerebellar ataxia, autosomal recessive 8; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 28
Download table as spreadsheet
HGVS dbSNP
NM_000153.4(GALC):c.1162-4del rs11300320
NM_000153.4(GALC):c.1987T>G (p.Trp663Gly) rs1060499761
NM_000170.2(GLDC):c.2938A>G (p.Asn980Asp) rs772574530
NM_001048166.1(STIL):c.1455G>C (p.Leu485Phe) rs139912214
NM_001111125.3(IQSEC2):c.3364C>T (p.Arg1122Cys) rs782697291
NM_001130438.3(SPTAN1):c.1330G>A (p.Val444Ile) rs77358650
NM_001360.2(DHCR7):c.278C>T (p.Thr93Met) rs80338853
NM_003560.4(PLA2G6):c.2129G>A (p.Arg710His) rs147455037
NM_005634.2(SOX3):c.157G>C (p.Val53Leu) rs200361128
NM_006295.3(VARS1):c.2653C>T (p.Leu885Phe) rs1060499734
NM_006295.3(VARS1):c.3173G>A (p.Arg1058Gln) rs769369302
NM_006651.4(CPLX1):c.322G>T (p.Glu108Ter) rs1060499735
NM_013438.5(UBQLN1):c.377del (p.Asn126fs) rs1060499753
NM_014363.6(SACS):c.2182C>T (p.Arg728Ter) rs752059006
NM_014363.6(SACS):c.4466A>G (p.Asn1489Ser) rs147099630
NM_016952.4(CDON):c.3395C>T (p.Pro1132Leu) rs754025360
NM_017882.3(CLN6):c.407G>A (p.Arg136His) rs769701646
NM_018245.3(OGDHL):c.2333C>T (p.Ser778Leu) rs773888308
NM_021222.3(PRUNE1):c.316G>A (p.Asp106Asn) rs773618224
NM_021222.3(PRUNE1):c.383G>A (p.Arg128Gln) rs767769359
NM_021222.3(PRUNE1):c.520G>T (p.Gly174Ter) rs200618384
NM_021222.3(PRUNE1):c.88G>A (p.Asp30Asn) rs1057521927
NM_022835.3(PLEKHG2):c.1708G>A (p.Gly570Arg) rs370673772
NM_024596.5(MCPH1):c.427dup (p.Thr143fs) rs199422125
NM_025137.4(SPG11):c.5175del (p.Ala1726fs) rs1060499768
NM_152269.5(C12orf65):c.248del (p.Val83fs) rs587776508
NM_176787.5(PIGN):c.996T>G (p.Ile332Met) rs1060499763
NM_182961.4(SYNE1):c.19692+3G>A rs150304757

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.