2-144520469-AC-ACCCCCCC

Variant names:

• chr2-144520469-A-ACCCCCC
• rs1303890891
• ENST00000637267.2:c.-340+81_-340+86dupGGGGGG

Variant summary

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

The ENST00000621340.1(ENSG00000273537):​n.17_22dupCCCCCC variant causes a 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 0.000020 (0 hom., cov: 0)
• Consequence: ENSG00000273537 ENST00000621340.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630
• Publications: 0 publications found

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-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]

ENSG00000273537 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621340.1. 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+187_284+192dupCCCCCC		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZEB2	ENST00000637267.2	TSL:5	c.-340+81_-340+86dupGGGGGG		intron	N/A	ENSP00000490293.2	A0A1X7SC99
	ZEB2-AS1	ENST00000427278.8	TSL:5	n.1008_1013dupCCCCCC		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000273537	ENST00000621340.1	TSL:6	n.17_22dupCCCCCC		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0000203 AC: 1 AN: 49378 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000353

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0000202 AC: 1 AN: 49416 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 21880

African (AFR) AF: 0.00 AC: 0 AN: 10308

American (AMR) AF: 0.00 AC: 0 AN: 4104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1666

East Asian (EAS) AF: 0.00 AC: 0 AN: 1034

South Asian (SAS) AF: 0.00 AC: 0 AN: 876

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2076

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 100

European-Non Finnish (NFE) AF: 0.0000353 AC: 1 AN: 28312

Other (OTH) AF: 0.00 AC: 0 AN: 634

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

Other links and lift over

dbSNP: rs1303890891; hg19: chr2-145278036;