rs180318

Variant summary

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

The NM_000211.5(ITGB2):​c.2081-678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,652 control chromosomes in the GnomAD database, including 38,096 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 0.70 ( 38096 hom., cov: 31)

Consequence

ITGB2
NM_000211.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.73
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITGB2NM_000211.5 linkuse as main transcriptc.2081-678A>G intron_variant ENST00000652462.1 NP_000202.3 P05107A0A494C0X7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITGB2ENST00000652462.1 linkuse as main transcriptc.2081-678A>G intron_variant NM_000211.5 ENSP00000498780.1 A0A494C0X7

Frequencies

GnomAD3 genomes
AF:
0.696
AC:
105466
AN:
151534
Hom.:
38031
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.891
Gnomad AMI
AF:
0.452
Gnomad AMR
AF:
0.627
Gnomad ASJ
AF:
0.613
Gnomad EAS
AF:
0.809
Gnomad SAS
AF:
0.689
Gnomad FIN
AF:
0.619
Gnomad MID
AF:
0.662
Gnomad NFE
AF:
0.604
Gnomad OTH
AF:
0.701
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.696
AC:
105597
AN:
151652
Hom.:
38096
Cov.:
31
AF XY:
0.696
AC XY:
51602
AN XY:
74110
show subpopulations
Gnomad4 AFR
AF:
0.892
Gnomad4 AMR
AF:
0.626
Gnomad4 ASJ
AF:
0.613
Gnomad4 EAS
AF:
0.808
Gnomad4 SAS
AF:
0.689
Gnomad4 FIN
AF:
0.619
Gnomad4 NFE
AF:
0.604
Gnomad4 OTH
AF:
0.706
Alfa
AF:
0.638
Hom.:
7069
Bravo
AF:
0.707

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.36
DANN
Benign
0.37

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.

Other links and lift over

dbSNP: rs180318; hg19: chr21-46307495; COSMIC: COSV56612321; API