rs161233

chr10-31461552-T-G

Variant summary

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

The NM_001174096.2(ZEB1):c.259+315T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 152,162 control chromosomes in the GnomAD database, including 661 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 0.078 (661 hom., cov: 32)
• Consequence: ZEB1 NM_001174096.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

ZEB1 (HGNC:11642): (zinc finger E-box binding homeobox 1) This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have been associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZEB1	NM_001174096.2	c.259+315T>G		intron_variant		ENST00000424869.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZEB1	ENST00000424869.6	c.259+315T>G		intron_variant		5	NM_001174096.2	A2

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11871 AN: 152044 Hom.: 661 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0781 AC: 11884 AN: 152162 Hom.: 661 Cov.: 32 AF XY: 0.0789 AC XY: 5868 AN XY: 74392

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.0463

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.0679 Hom.: 56

Bravo AF: 0.0792

Asia WGS AF: 0.0340 AC: 117 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	13
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs161233; hg19: chr10-31750481;