Variant rs2272300 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.*6094T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,580,096 control chromosomes in the GnomAD database, including 17,072 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 0.21 ( 5408 hom., cov: 31)

Exomes 𝑓: 0.10 ( 11664 hom. )

Consequence

ZNF740
NM_001004304.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

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:

ITGB7 (HGNC:):

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF740	NM_001004304.4 linkuse as main transcript	c.*6094T>G		3_prime_UTR_variant	7/7	ENST00000416904.5	NP_001004304.1	Q8NDX6
ITGB7	NM_000889.3 linkuse as main transcript	c.1502+24A>C		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 linkuse as main transcript	c.*6094T>G		3_prime_UTR_variant	7/7	1	NM_001004304.4	ENSP00000409463.2		Q8NDX6
ITGB7	ENST00000267082.10 linkuse as main transcript	c.1502+24A>C		intron_variant		1	NM_000889.3	ENSP00000267082.4		P26010-1

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31475

AN:

151756

Hom.:

5386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.150

Gnomad NFE

AF:

0.0867

Gnomad OTH

AF:

0.169

GnomAD3 exomes

AF:

0.141

AC:

32124

AN:

228348

Hom.:

3504

AF XY:

0.137

AC XY:

16798

AN XY:

122728

show subpopulations

Gnomad AFR exome

AF:

0.485

Gnomad AMR exome

AF:

0.0612

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.162

Gnomad SAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.0921

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.103

AC:

147775

AN:

1428222

Hom.:

11664

Cov.:

AF XY:

0.105

AC XY:

74485

AN XY:

706948

show subpopulations

Gnomad4 AFR exome

AF:

0.495

Gnomad4 AMR exome

AF:

0.0666

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.0793

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.208

AC:

31553

AN:

151874

Hom.:

5408

Cov.:

AF XY:

0.208

AC XY:

15406

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.103

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.226

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.0867

Gnomad4 OTH

AF:

0.174

Alfa

AF:

0.119

Hom.:

1059

Bravo

AF:

0.214

Asia WGS

AF:

0.234

AC:

815

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.2

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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