GeneBe

rs35231134

Variant names:

Variant summary

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

The ENST00000453237.5(CXCR2):​c.-141+224_-141+226delTTT 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 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CXCR2
ENST00000453237.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.929

Publications

0 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+232_-141+234delTTT intron_variant Intron 1 of 3 NP_001161770.1
CXCR2XM_047444190.1 linkc.-89+232_-89+234delTTT intron_variant Intron 1 of 2 XP_047300146.1
CXCR2XM_047444187.1 linkc.-339_-337delTTT upstream_gene_variant XP_047300143.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CXCR2ENST00000453237.5 linkc.-141+224_-141+226delTTT intron_variant Intron 1 of 3 1 ENSP00000413686.1
CXCR2ENST00000449014.5 linkc.-339_-337delTTT upstream_gene_variant 1 ENSP00000410506.1
CXCR2ENST00000415392.5 linkc.-268_-266delTTT upstream_gene_variant 5 ENSP00000392348.1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
148142
Hom.:
0
Cov.:
0
Gnomad AFR
AF:
0.00
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
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
24
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
16
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
16
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
6
Other (OTH)
AF:
0.00
AC:
0
AN:
2
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
148142
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
72100
African (AFR)
AF:
0.00
AC:
0
AN:
40336
American (AMR)
AF:
0.00
AC:
0
AN:
14864
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3418
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5008
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4672
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9836
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
66786
Other (OTH)
AF:
0.00
AC:
0
AN:
2024
Alfa
AF:
0.00
Hom.:
521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.93

Splicing

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

Publications

Other links and lift over

dbSNP: rs35231134; hg19: chr2-218990305; API