GeneBe

ENST00000453237.5:c.-141+217_-141+218insT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000453237.5(CXCR2):​c.-141+217_-141+218insT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)

Consequence

CXCR2
ENST00000453237.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.467

Publications

1 publications found
Variant links:
Genes affected
CXCR2 (HGNC:6027): (C-X-C motif chemokine receptor 2) The protein encoded by this gene is a member of the G-protein-coupled receptor family. This protein is a receptor for interleukin 8 (IL8). It binds to IL8 with high affinity, and transduces the signal through a G-protein activated second messenger system. This receptor also binds to chemokine (C-X-C motif) ligand 1 (CXCL1/MGSA), a protein with melanoma growth stimulating activity, and has been shown to be a major component required for serum-dependent melanoma cell growth. This receptor mediates neutrophil migration to sites of inflammation. The angiogenic effects of IL8 in intestinal microvascular endothelial cells are found to be mediated by this receptor. Knockout studies in mice suggested that this receptor controls the positioning of oligodendrocyte precursors in developing spinal cord by arresting their migration. This gene, IL8RA, a gene encoding another high affinity IL8 receptor, as well as IL8RBP, a pseudogene of IL8RB, form a gene cluster in a region mapped to chromosome 2q33-q36. Alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2009]
CXCR2 Gene-Disease associations (from GenCC):
  • WHIM syndrome 2
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • autosomal recessive severe congenital neutropenia due to CXCR2 deficiency
    Inheritance: AR Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CXCR2NM_001168298.2 linkc.-141+222dupT intron_variant Intron 1 of 3 NP_001161770.1 P25025Q53PC4
CXCR2XM_047444190.1 linkc.-89+222dupT intron_variant Intron 1 of 2 XP_047300146.1
CXCR2XM_047444187.1 linkc.-346_-345insT upstream_gene_variant XP_047300143.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CXCR2ENST00000453237.5 linkc.-141+217_-141+218insT intron_variant Intron 1 of 3 1 ENSP00000413686.1 C9JW47
CXCR2ENST00000449014.5 linkc.-346_-345insT upstream_gene_variant 1 ENSP00000410506.1 Q6LCZ7
CXCR2ENST00000415392.5 linkc.-275_-274insT upstream_gene_variant 5 ENSP00000392348.1 C9J2F9

Frequencies

GnomAD3 genomes
AF:
0.00000663
AC:
1
AN:
150762
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000244
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000663
AC:
1
AN:
150762
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
73524
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000244
AC:
1
AN:
40952
American (AMR)
AF:
0.00
AC:
0
AN:
15180
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3444
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5144
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4746
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10394
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67618
Other (OTH)
AF:
0.00
AC:
0
AN:
2076
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs45493792; hg19: chr2-218990299; API