Variant 17-3751686-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000263087.9(ITGAE):c.1857T>C(p.Asn619=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,613,798 control chromosomes in the GnomAD database, including 11,366 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 0.13 ( 1457 hom., cov: 31)

Exomes 𝑓: 0.11 ( 9909 hom. )

Consequence

ITGAE
ENST00000263087.9 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Variant links:

Genes affected

ITGAE (HGNC:6147): (integrin subunit alpha E) Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This gene encodes an I-domain-containing alpha integrin that undergoes post-translational cleavage in the extracellular domain, yielding disulfide-linked heavy and light chains. In combination with the beta 7 integrin, this protein forms the E-cadherin binding integrin known as the human mucosal lymphocyte-1 antigen. This protein is preferentially expressed in human intestinal intraepithelial lymphocytes (IEL), and in addition to a role in adhesion, it may serve as an accessory molecule for IEL activation. [provided by RefSeq, Jul 2008]

ITGAE links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP7

Synonymous conserved (PhyloP=-1.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGAE	NM_002208.5 linkuse as main transcript	c.1857T>C	p.Asn619=	synonymous_variant	15/31	ENST00000263087.9	NP_002199.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGAE	ENST00000263087.9 linkuse as main transcript	c.1857T>C	p.Asn619=	synonymous_variant	15/31	1	NM_002208.5	ENSP00000263087	P1

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19873

AN:

151916

Hom.:

1441

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0970

Gnomad OTH

AF:

0.119

GnomAD3 exomes

AF:

0.124

AC:

31162

AN:

251380

Hom.:

2095

AF XY:

0.124

AC XY:

16861

AN XY:

135850

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.0906

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.162

Gnomad SAS exome

AF:

0.156

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.0987

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.111

AC:

161907

AN:

1461764

Hom.:

9909

Cov.:

AF XY:

0.112

AC XY:

81725

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.169

Gnomad4 AMR exome

AF:

0.0904

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.218

Gnomad4 SAS exome

AF:

0.159

Gnomad4 FIN exome

AF:

0.189

Gnomad4 NFE exome

AF:

0.0973

Gnomad4 OTH exome

AF:

0.116

GnomAD4 genome

AF:

0.131

AC:

19926

AN:

152034

Hom.:

1457

Cov.:

AF XY:

0.136

AC XY:

10130

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.170

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.0969

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.104

Hom.:

1804

Bravo

AF:

0.125

Asia WGS

AF:

0.146

AC:

509

AN:

3478

EpiCase

AF:

0.0974

EpiControl

AF:

0.0988

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.031

DANN

Benign

0.30

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

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