21-44906962-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000211.5(ITGB2):​c.281G>C​(p.Gly94Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

ITGB2
NM_000211.5 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.03
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.086596906).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITGB2NM_000211.5 linkc.281G>C p.Gly94Ala missense_variant 4/16 ENST00000652462.1 NP_000202.3 P05107A0A494C0X7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITGB2ENST00000652462.1 linkc.281G>C p.Gly94Ala missense_variant 4/16 NM_000211.5 ENSP00000498780.1 A0A494C0X7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251458
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.064
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
0.14
DANN
Benign
0.52
DEOGEN2
Benign
0.31
.;.;T;.;.;.;.;.;T;.;T;T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.070
N
LIST_S2
Benign
0.54
.;.;T;.;.;T;T;T;T;T;T;T
M_CAP
Benign
0.063
D
MetaRNN
Benign
0.087
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.61
T
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-0.99
N;N;N;N;N;N;N;N;N;N;D;D
REVEL
Benign
0.21
Sift
Benign
0.30
T;T;T;T;T;T;T;T;T;T;T;T
Sift4G
Benign
0.40
T;T;T;T;T;T;T;.;T;.;.;T
Vest4
0.19
MutPred
0.25
Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);.;Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);.;.;
MVP
0.73
MPC
0.35
ClinPred
0.057
T
GERP RS
-4.2
gMVP
0.28

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: rs761719553; hg19: chr21-46326877; API