rs567229506

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_014795.4(ZEB2):​c.*35delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000746 in 1,580,884 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000067 ( 0 hom. )

Consequence

ZEB2
NM_014795.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.27
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6
Variant 2-144389415-GA-G is Benign according to our data. Variant chr2-144389415-GA-G is described in Lovd as [Benign].
BS2
High AC in GnomAd4 at 22 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZEB2NM_014795.4 linkc.*35delT 3_prime_UTR_variant Exon 10 of 10 ENST00000627532.3 NP_055610.1 O60315-1
ZEB2NM_001171653.2 linkc.*35delT 3_prime_UTR_variant Exon 9 of 9 NP_001165124.1 O60315-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZEB2ENST00000627532 linkc.*35delT 3_prime_UTR_variant Exon 10 of 10 1 NM_014795.4 ENSP00000487174.1 O60315-1

Frequencies

GnomAD3 genomes
AF:
0.000147
AC:
22
AN:
150064
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000441
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000265
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000671
AC:
96
AN:
1430704
Hom.:
0
Cov.:
30
AF XY:
0.0000757
AC XY:
54
AN XY:
713092
show subpopulations
Gnomad4 AFR exome
AF:
0.000304
Gnomad4 AMR exome
AF:
0.000763
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.0000234
Gnomad4 FIN exome
AF:
0.0000759
Gnomad4 NFE exome
AF:
0.0000369
Gnomad4 OTH exome
AF:
0.0000842
GnomAD4 genome
AF:
0.000146
AC:
22
AN:
150180
Hom.:
0
Cov.:
32
AF XY:
0.000109
AC XY:
8
AN XY:
73228
show subpopulations
Gnomad4 AFR
AF:
0.000439
Gnomad4 AMR
AF:
0.000264
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs567229506; hg19: chr2-145146982; API