Variant rs11170466 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001004304.4(ZNF740):c.*4485C>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 0.0579 in 1,566,724 control chromosomes in the GnomAD database, including 3,223 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 0.059 ( 354 hom., cov: 32)

Exomes 𝑓: 0.058 ( 2869 hom. )

Consequence

ZNF740
NM_001004304.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.137

Variant links:

Genes affected

ZNF740 (HGNC:27465): (zinc finger protein 740) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ZNF740 links:

ITGB7 (HGNC:6162): (integrin subunit beta 7) This gene encodes a protein that is a member of the integrin superfamily. Members of this family are adhesion receptors that function in signaling from the extracellular matrix to the cell. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. The encoded protein forms dimers with an alpha4 chain or an alphaE chain and plays a role in leukocyte adhesion. Dimerization with alpha4 forms a homing receptor for migration of lymphocytes to the intestinal mucosa and Peyer's patches. Dimerization with alphaE permits binding to the ligand epithelial cadherin, a calcium-dependent adhesion molecule. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013]

ITGB7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF740	NM_001004304.4 link	c.*4485C>T		3_prime_UTR_variant	7/7	ENST00000416904.5	NP_001004304.1	Q8NDX6
ITGB7	NM_000889.3 link	c.2156-56G>A		intron_variant		ENST00000267082.10	NP_000880.1	P26010-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF740	ENST00000416904.5 link	c.*4485C>T		3_prime_UTR_variant	7/7	1	NM_001004304.4	ENSP00000409463.2		Q8NDX6
ITGB7	ENST00000267082.10 link	c.2156-56G>A		intron_variant		1	NM_000889.3	ENSP00000267082.4		P26010-1

Frequencies

GnomAD3 genomes

AF:

0.0593

AC:

9026

AN:

152082

Hom.:

354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0350

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.0338

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.0361

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0606

Gnomad OTH

AF:

0.0564

GnomAD4 exome

AF:

0.0578

AC:

81704

AN:

1414524

Hom.:

2869

Cov.:

AF XY:

0.0573

AC XY:

40197

AN XY:

701280

show subpopulations

Gnomad4 AFR exome

AF:

0.0367

Gnomad4 AMR exome

AF:

0.0271

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.174

Gnomad4 SAS exome

AF:

0.0313

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.0534

Gnomad4 OTH exome

AF:

0.0620

GnomAD4 genome

AF:

0.0593

AC:

9023

AN:

152200

Hom.:

354

Cov.:

AF XY:

0.0617

AC XY:

4592

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0350

Gnomad4 AMR

AF:

0.0338

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.0359

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.0606

Gnomad4 OTH

AF:

0.0553

Alfa

AF:

0.0597

Hom.:

304

Bravo

AF:

0.0517

Asia WGS

AF:

0.0650

AC:

226

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.4

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over