21-44924735-A-G

Variant summary

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

The NM_001127491.3(ITGB2):​c.-4+3919T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,080 control chromosomes in the GnomAD database, including 27,974 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 0.58 ( 27974 hom., cov: 32)

Consequence

ITGB2
NM_001127491.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.53
Variant links:
Genes affected
ITGB2-AS1 (HGNC:44304): (ITGB2 antisense RNA 1)
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITGB2NM_001127491.3 linkc.-4+3919T>C intron_variant NP_001120963.2 P05107A0A494C0X7
ITGB2-AS1NR_038311.1 linkn.388+1752A>G intron_variant
ITGB2-AS1NR_038312.1 linkn.388+1752A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITGB2-AS1ENST00000441379.5 linkn.278-2133A>G intron_variant 1
ITGB2ENST00000355153.8 linkc.-4+3919T>C intron_variant 2 ENSP00000347279.4 P05107
ITGB2ENST00000397850.6 linkc.-233-3685T>C intron_variant 5 ENSP00000380948.2 P05107

Frequencies

GnomAD3 genomes
AF:
0.577
AC:
87729
AN:
151962
Hom.:
27914
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.863
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.564
Gnomad ASJ
AF:
0.508
Gnomad EAS
AF:
0.434
Gnomad SAS
AF:
0.389
Gnomad FIN
AF:
0.436
Gnomad MID
AF:
0.601
Gnomad NFE
AF:
0.457
Gnomad OTH
AF:
0.551
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.578
AC:
87860
AN:
152080
Hom.:
27974
Cov.:
32
AF XY:
0.573
AC XY:
42560
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.863
Gnomad4 AMR
AF:
0.564
Gnomad4 ASJ
AF:
0.508
Gnomad4 EAS
AF:
0.436
Gnomad4 SAS
AF:
0.388
Gnomad4 FIN
AF:
0.436
Gnomad4 NFE
AF:
0.457
Gnomad4 OTH
AF:
0.552
Alfa
AF:
0.459
Hom.:
3072
Bravo
AF:
0.607
Asia WGS
AF:
0.451
AC:
1570
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.2
DANN
Benign
0.28

Splicing

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: rs2838739; hg19: chr21-46344650; API