rs7349

chr10-31528977-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.*1713C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,094 control chromosomes in the GnomAD database, including 14,102 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 0.28 (14102 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZEB1 NM_001174096.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

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=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZEB1	NM_001174096.2	c.*1713C>T		3_prime_UTR_variant	9/9	ENST00000424869.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZEB1	ENST00000424869.6	c.*1713C>T		3_prime_UTR_variant	9/9	5	NM_001174096.2	A2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42224 AN: 151976 Hom.: 14043 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.223

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.278 AC: 42330 AN: 152094 Hom.: 14102 Cov.: 32 AF XY: 0.273 AC XY: 20329 AN XY: 74362

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0655

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0716

Gnomad4 NFE AF: 0.0542

Gnomad4 OTH AF: 0.221

Alfa AF: 0.0875 Hom.: 3405

Bravo AF: 0.307

Asia WGS AF: 0.193 AC: 671 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	14
Dann	Benign	0.85

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: rs7349; hg19: chr10-31817905;