rs12242798

chr10-31289989-G-Achr10-31289989-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605946.1(ZEB1-AS1):n.177+29526C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 151,998 control chromosomes in the GnomAD database, including 2,645 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 0.11 (2645 hom., cov: 32)
• Consequence: ZEB1-AS1 ENST00000605946.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZEB1-AS1	ENST00000605946.1	n.177+29526C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17028 AN: 151880 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.00973

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.112 AC: 17072 AN: 151998 Hom.: 2645 Cov.: 32 AF XY: 0.109 AC XY: 8067 AN XY: 74306

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.0966

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.0791

Gnomad4 FIN AF: 0.00340

Gnomad4 NFE AF: 0.00971

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0255 Hom.: 345

Bravo AF: 0.126

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.6
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12242798; hg19: chr10-31578918;