dbSNP rs1303890891: ZEB2:c.-340+86delG (chr2-144520469-AC-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000637267.2(ZEB2):c.-340+86delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00026 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

ZEB2
ENST00000637267.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.630

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]

ZEB2 links:

ZEB2-AS1 (HGNC:37149): (ZEB2 antisense RNA 1) This gene produces a spliced long non-coding RNA which is a natural antisense transcript corresponding to the 5' UTR of zinc finger E-box binding homeobox 2 (ZEB2). It is thought that this transcript may be involved in the regulation of ZEB2 expression, and may play a role in the progression of bladder cancer. [provided by RefSeq, Aug 2015]

ZEB2-AS1 links:

ENSG00000273537 (HGNC:):

ENSG00000273537 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAd4 at 13 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZEB2-AS1	NR_040248.2 link	n.284+192delC		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ZEB2	ENST00000637267.2 link	c.-340+86delG	intron_variant	Intron 1 of 8	5	ENSP00000490293.2	A0A1X7SC99
ZEB2-AS1	ENST00000427278.8 link	n.1013delC	non_coding_transcript_exon_variant	Exon 3 of 3	5
ENSG00000273537	ENST00000621340.1 link	n.22delC	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.000263

AC:

AN:

49378

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000973

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000245

Gnomad ASJ

AF:

0.000600

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000353

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000112

AC:

AN:

196846

Hom.:

Cov.:

AF XY:

0.000101

AC XY:

AN XY:

109040

show subpopulations

Gnomad4 AFR exome

AF:

0.000388

Gnomad4 AMR exome

AF:

0.000519

Gnomad4 ASJ exome

AF:

0.000231

Gnomad4 EAS exome

AF:

0.000247

Gnomad4 SAS exome

AF:

0.0000507

Gnomad4 FIN exome

AF:

0.000121

Gnomad4 NFE exome

AF:

0.0000637

Gnomad4 OTH exome

AF:

0.000106

GnomAD4 genome

AF:

0.000263

AC:

AN:

49416

Hom.:

Cov.:

AF XY:

0.000229

AC XY:

AN XY:

21880

show subpopulations

Gnomad4 AFR

AF:

0.000970

Gnomad4 AMR

AF:

0.000244

Gnomad4 ASJ

AF:

0.000600

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000353

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over