rs2839659

chr10-31380865-C-T

Variant summary

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

The NM_001174096.2(ZEB1):c.58+61573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,970 control chromosomes in the GnomAD database, including 8,232 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 0.29 (8232 hom., cov: 32)
• Consequence: ZEB1 NM_001174096.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZEB1	NM_001174096.2	c.58+61573C>T		intron_variant		ENST00000424869.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZEB1	ENST00000424869.6	c.58+61573C>T		intron_variant		5	NM_001174096.2	A2

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44746 AN: 151852 Hom.: 8226 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44752 AN: 151970 Hom.: 8232 Cov.: 32 AF XY: 0.294 AC XY: 21802 AN XY: 74264

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.313

Alfa AF: 0.303 Hom.: 1499

Bravo AF: 0.280

Asia WGS AF: 0.323 AC: 1123 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.23
Dann	Benign	0.67

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: rs2839659; hg19: chr10-31669794;