chr10-31289989-G-A

Variant names:

• chr10-31289989-G-A
• rs12242798
• ENST00000605946.1:n.177+29526C>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+29526C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605946.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZEB1-AS1	ENST00000605946.1	TSL:5	n.177+29526C>T		intron	N/A
	ZEB1-AS1	ENST00000805106.1		n.202+30294C>T		intron	N/A

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

African (AFR) AF: 0.348 AC: 14426 AN: 41428

American (AMR) AF: 0.0573 AC: 872 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0966 AC: 335 AN: 3468

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5176

South Asian (SAS) AF: 0.0791 AC: 382 AN: 4828

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.00971 AC: 660 AN: 67952

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0377 Hom.: 905

Bravo AF: 0.126

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		0.080
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12242798; hg19: chr10-31578918;