chr2-144384605-C-CTTT
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_014795.4(ZEB2):c.*4843_*4845dupAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000704 in 142,106 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 29)
Consequence
ZEB2
NM_014795.4 3_prime_UTR
NM_014795.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.35
Publications
1 publications found
Genes affected
ZEB2 (HGNC:14881): (zinc finger E-box binding homeobox 2) The protein encoded by this gene is a member of the Zfh1 family of 2-handed zinc finger/homeodomain proteins. It is located in the nucleus and functions as a DNA-binding transcriptional repressor that interacts with activated SMADs. Mutations in this gene are associated with Hirschsprung disease/Mowat-Wilson syndrome. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jan 2010]
ZEB2 Gene-Disease associations (from GenCC):
- Mowat-Wilson syndromeInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000704 AC: 1AN: 142106Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
142106
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome AF: 0.00000704 AC: 1AN: 142106Hom.: 0 Cov.: 29 AF XY: 0.0000145 AC XY: 1AN XY: 68936 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
142106
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
68936
show subpopulations
African (AFR)
AF:
AC:
0
AN:
38714
American (AMR)
AF:
AC:
0
AN:
14200
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3316
East Asian (EAS)
AF:
AC:
0
AN:
4984
South Asian (SAS)
AF:
AC:
0
AN:
4570
European-Finnish (FIN)
AF:
AC:
1
AN:
8626
Middle Eastern (MID)
AF:
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
AC:
0
AN:
64582
Other (OTH)
AF:
AC:
0
AN:
1922
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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