10-31415994-T-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001174096.2(ZEB1):c.59-45043T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,000 control chromosomes in the GnomAD database, including 14,187 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 0.28 ( 14187 hom., cov: 32)
Consequence
ZEB1
NM_001174096.2 intron
NM_001174096.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0610
Publications
1 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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.283 AC: 42933AN: 151880Hom.: 14129 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
42933
AN:
151880
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: 0.283 AC: 43036AN: 152000Hom.: 14187 Cov.: 32 AF XY: 0.278 AC XY: 20689AN XY: 74312 show subpopulations
GnomAD4 genome
AF:
AC:
43036
AN:
152000
Hom.:
Cov.:
32
AF XY:
AC XY:
20689
AN XY:
74312
show subpopulations
African (AFR)
AF:
AC:
33355
AN:
41470
American (AMR)
AF:
AC:
2131
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
515
AN:
3468
East Asian (EAS)
AF:
AC:
1068
AN:
5174
South Asian (SAS)
AF:
AC:
779
AN:
4818
European-Finnish (FIN)
AF:
AC:
764
AN:
10598
Middle Eastern (MID)
AF:
AC:
56
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3874
AN:
67892
Other (OTH)
AF:
AC:
484
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
743
1486
2229
2972
3715
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
678
AN:
3462
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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