rs372501675

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_000211.5(ITGB2):c.453C>T(p.Gly151Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00017 ( 0 hom. )

Consequence

ITGB2
NM_000211.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.25

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

leukocyte adhesion deficiency 1
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

ITGB2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 21-44903411-G-A is Benign according to our data. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44903411-G-A is described in CliVar as Likely_benign. Clinvar id is 530693.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.25 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB2	NM_000211.5 link	c.453C>T	p.Gly151Gly	synonymous_variant	Exon 5 of 16	ENST00000652462.1	NP_000202.3	P05107A0A494C0X7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB2	ENST00000652462.1 link	c.453C>T	p.Gly151Gly	synonymous_variant	Exon 5 of 16		NM_000211.5	ENSP00000498780.1		A0A494C0X7

Frequencies

GnomAD3 genomes

AF:

0.000197

AC:

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000309

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000151

AC:

AN:

251462

AF XY:

0.000155

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.000211

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000171

AC:

250

AN:

1461838

Hom.:

Cov.:

AF XY:

0.000172

AC XY:

125

AN XY:

727228

show subpopulations

African (AFR)

AF:

0.000149

AC:

AN:

33478

American (AMR)

AF:

0.000157

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26134

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39700

South Asian (SAS)

AF:

0.0000232

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.0000562

AC:

AN:

53416

Middle Eastern (MID)

AF:

0.000173

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.000202

AC:

225

AN:

1111970

Other (OTH)

AF:

0.0000993

AC:

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000197

AC:

AN:

152152

Hom.:

Cov.:

AF XY:

0.000148

AC XY:

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.000193

AC:

AN:

41420

American (AMR)

AF:

0.00

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.000309

AC:

AN:

68020

Other (OTH)

AF:

0.00

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000276

Hom.:

Bravo

AF:

0.000159

EpiCase

AF:

0.000382

EpiControl

AF:

0.000237

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

ITGB2: BP4, BP7 -

Leukocyte adhesion deficiency 1

Benign:1

Dec 08, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.14

(source)

DANN

Benign

0.59

PhyloP100

-4.3

Mutation Taster

=92/8

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over