ENST00000605946.1:n.177+27839G>T

Variant names:

• chr10-31291676-C-A
• rs16932309
• ENST00000605946.1:n.177+27839G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605946.1(ZEB1-AS1):​n.177+27839G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,830 control chromosomes in the GnomAD database, including 2,737 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (2737 hom., cov: 31)
• Consequence: ZEB1-AS1 ENST00000605946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515
• Publications: 3 publications found

Genes affected

ZEB1-AS1 (HGNC:42354): (ZEB1 antisense RNA 1) This locus produces long non-coding RNA that is transcribed from a shared bi-directional promoter with zinc finger E-box binding homeobox 1 (ZEB1). This transcript binds lysine methyltransferase 2A and promotes histone modifications that are thought to promote expression of ZEB1. Expression of this gene is correlated with tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZEB1-AS1	ENST00000605946.1	n.177+27839G>T		intron_variant	Intron 1 of 1	5
ZEB1-AS1	ENST00000805106.1	n.202+28607G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20957 AN: 151712 Hom.: 2720 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0471

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 21010 AN: 151830 Hom.: 2737 Cov.: 31 AF XY: 0.139 AC XY: 10328 AN XY: 74212

African (AFR) AF: 0.345 AC: 14286 AN: 41404

American (AMR) AF: 0.0662 AC: 1007 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3470

East Asian (EAS) AF: 0.179 AC: 924 AN: 5160

South Asian (SAS) AF: 0.0853 AC: 411 AN: 4816

European-Finnish (FIN) AF: 0.0690 AC: 729 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0471 AC: 3199 AN: 67882

Other (OTH) AF: 0.114 AC: 240 AN: 2104

Alfa AF: 0.109 Hom.: 332

Bravo AF: 0.149

Asia WGS AF: 0.118 AC: 409 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.7
DANN	Benign	0.38
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs16932309; hg19: chr10-31580605;