Variant rs3746972 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000211.5(ITGB2):c.148-825T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 591,072 control chromosomes in the GnomAD database, including 8,693 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2368 hom., cov: 33)

Exomes 𝑓: 0.16 ( 6325 hom. )

Consequence

ITGB2
NM_000211.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.206

Variant links:

Genes affected

ITGB2 (HGNC:6155): (integrin subunit beta 2) This gene encodes an integrin beta chain, which combines with multiple different alpha chains to form different integrin heterodimers. Integrins are integral cell-surface proteins that participate in cell adhesion as well as cell-surface mediated signalling. The encoded protein plays an important role in immune response and defects in this gene cause leukocyte adhesion deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

ITGB2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 21-44907920-A-G is Benign according to our data. Variant chr21-44907920-A-G is described in ClinVar as [Benign]. Clinvar id is 2688237.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB2	NM_000211.5 linkuse as main transcript	c.148-825T>C		intron_variant		ENST00000652462.1	NP_000202.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB2	ENST00000652462.1 linkuse as main transcript	c.148-825T>C		intron_variant			NM_000211.5	ENSP00000498780	P1

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25908

AN:

152170

Hom.:

2371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.0894

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.153

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.167

GnomAD4 exome

AF:

0.164

AC:

72060

AN:

438784

Hom.:

6325

AF XY:

0.160

AC XY:

37301

AN XY:

232866

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.184

Gnomad4 EAS exome

AF:

0.110

Gnomad4 SAS exome

AF:

0.0939

Gnomad4 FIN exome

AF:

0.176

Gnomad4 NFE exome

AF:

0.175

Gnomad4 OTH exome

AF:

0.172

GnomAD4 genome

AF:

0.170

AC:

25913

AN:

152288

Hom.:

2368

Cov.:

AF XY:

0.171

AC XY:

12745

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.131

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.0889

Gnomad4 FIN

AF:

0.184

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.180

Hom.:

3333

Bravo

AF:

0.174

Asia WGS

AF:

0.131

AC:

456

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied by a panel of primary immunodeficiencies. Number of patients: 30. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.64

DANN

Benign

0.68

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over