chr10-31466930-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001174096.2(ZEB1):c.259+5693C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 152,052 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.015 ( 53 hom., cov: 32)
Consequence
ZEB1
NM_001174096.2 intron
NM_001174096.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.805
Publications
2 publications found
Genes affected
ZEB1 (HGNC:11642): (zinc finger E-box binding homeobox 1) This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have been associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2010]
ZEB1 Gene-Disease associations (from GenCC):
- posterior polymorphous corneal dystrophy 3Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- Fuchs' endothelial dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- posterior polymorphous corneal dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- corneal dystrophy, Fuchs endothelial, 6Inheritance: AD Classification: LIMITED Submitted by: G2P
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0151 (2291/152052) while in subpopulation AFR AF = 0.0508 (2105/41464). AF 95% confidence interval is 0.049. There are 53 homozygotes in GnomAd4. There are 1093 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 2291 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0150 AC: 2286AN: 151934Hom.: 54 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2286
AN:
151934
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0151 AC: 2291AN: 152052Hom.: 53 Cov.: 32 AF XY: 0.0147 AC XY: 1093AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
2291
AN:
152052
Hom.:
Cov.:
32
AF XY:
AC XY:
1093
AN XY:
74344
show subpopulations
African (AFR)
AF:
AC:
2105
AN:
41464
American (AMR)
AF:
AC:
110
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
1
AN:
4808
European-Finnish (FIN)
AF:
AC:
0
AN:
10562
Middle Eastern (MID)
AF:
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
AC:
34
AN:
67978
Other (OTH)
AF:
AC:
36
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
111
221
332
442
553
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
24
48
72
96
120
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
21
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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