chr10-31276426-A-G

Variant names:

• chr10-31276426-A-G
• rs1314013
• ENST00000605946.1:n.177+43089T>C

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+43089T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,190 control chromosomes in the GnomAD database, including 5,852 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 0.19 (5852 hom., cov: 32)
• Consequence: ZEB1-AS1 ENST00000605946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 9 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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+43089T>C		intron_variant	Intron 1 of 1	5
ZEB1-AS1	ENST00000805106.1	n.202+43857T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28412 AN: 152072 Hom.: 5814 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0480

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.187 AC: 28502 AN: 152190 Hom.: 5852 Cov.: 32 AF XY: 0.185 AC XY: 13794 AN XY: 74410

African (AFR) AF: 0.513 AC: 21289 AN: 41464

American (AMR) AF: 0.0850 AC: 1300 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0668 AC: 232 AN: 3472

East Asian (EAS) AF: 0.179 AC: 928 AN: 5178

South Asian (SAS) AF: 0.0858 AC: 414 AN: 4826

European-Finnish (FIN) AF: 0.0689 AC: 732 AN: 10620

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0479 AC: 3260 AN: 68020

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.0867 Hom.: 886

Bravo AF: 0.205

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.017
DANN	Benign	0.26
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1314013; hg19: chr10-31565355;