dbSNP rs1303890891: ZEB2:c.-340+86delG (chr2-144520469-AC-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000648781.1(ZEB2-AS1):n.651delC variant causes a splice region, non coding transcript exon 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-AS1
ENST00000648781.1 splice_region, non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.630

Publications

0 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648781.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZEB2-AS1	NR_040248.2		n.284+192delC		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZEB2	ENST00000637267.2	TSL:5	c.-340+86delG	intron	N/A	ENSP00000490293.2	A0A1X7SC99
ZEB2-AS1	ENST00000427278.8	TSL:5	n.1013delC	non_coding_transcript_exon	Exon 3 of 3
ENSG00000273537	ENST00000621340.1	TSL:6	n.22delC	non_coding_transcript_exon	Exon 1 of 1

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

African (AFR)

AF:

0.000388

AC:

AN:

5150

American (AMR)

AF:

0.000519

AC:

AN:

11568

Ashkenazi Jewish (ASJ)

AF:

0.000231

AC:

AN:

4338

East Asian (EAS)

AF:

0.000247

AC:

AN:

8108

South Asian (SAS)

AF:

0.0000507

AC:

AN:

39446

European-Finnish (FIN)

AF:

0.000121

AC:

AN:

8296

Middle Eastern (MID)

AF:

0.00

AC:

AN:

636

European-Non Finnish (NFE)

AF:

0.0000637

AC:

AN:

109874

Other (OTH)

AF:

0.000106

AC:

AN:

9430

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000263

AC:

AN:

49416

Hom.:

Cov.:

AF XY:

0.000229

AC XY:

AN XY:

21880

show subpopulations

African (AFR)

AF:

0.000970

AC:

AN:

10308

American (AMR)

AF:

0.000244

AC:

AN:

4104

Ashkenazi Jewish (ASJ)

AF:

0.000600

AC:

AN:

1666

East Asian (EAS)

AF:

0.00

AC:

AN:

1034

South Asian (SAS)

AF:

0.00

AC:

AN:

876

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2076

Middle Eastern (MID)

AF:

0.00

AC:

AN:

100

European-Non Finnish (NFE)

AF:

0.0000353

AC:

AN:

28312

Other (OTH)

AF:

0.00

AC:

AN:

634

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.63

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over