chr10-31461077-AGAT-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBS1BS2
The NM_001174096.2(ZEB1):c.105_107del(p.Asp35del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,613,390 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0070 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00091 ( 13 hom. )
Consequence
ZEB1
NM_001174096.2 inframe_deletion
NM_001174096.2 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.12
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001174096.2. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
Variant 10-31461077-AGAT-A is Benign according to our data. Variant chr10-31461077-AGAT-A is described in ClinVar as [Benign]. Clinvar id is 785316.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00698 (1063/152264) while in subpopulation AFR AF= 0.0235 (977/41572). AF 95% confidence interval is 0.0223. There are 12 homozygotes in gnomad4. There are 507 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1059 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZEB1 | NM_001174096.2 | c.105_107del | p.Asp35del | inframe_deletion | 2/9 | ENST00000424869.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZEB1 | ENST00000424869.6 | c.105_107del | p.Asp35del | inframe_deletion | 2/9 | 5 | NM_001174096.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00696 AC: 1059AN: 152146Hom.: 12 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1059
AN:
152146
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:
GnomAD3 exomes AF: 0.00205 AC: 514AN: 250904Hom.: 6 AF XY: 0.00159 AC XY: 215AN XY: 135616
GnomAD3 exomes
AF:
AC:
514
AN:
250904
Hom.:
AF XY:
AC XY:
215
AN XY:
135616
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000905 AC: 1323AN: 1461126Hom.: 13 AF XY: 0.000805 AC XY: 585AN XY: 726864
GnomAD4 exome
AF:
AC:
1323
AN:
1461126
Hom.:
AF XY:
AC XY:
585
AN XY:
726864
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00698 AC: 1063AN: 152264Hom.: 12 Cov.: 32 AF XY: 0.00681 AC XY: 507AN XY: 74456
GnomAD4 genome
?
AF:
AC:
1063
AN:
152264
Hom.:
Cov.:
32
AF XY:
AC XY:
507
AN XY:
74456
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
4
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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