rs17844765
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001557.4(CXCR2):c.*355C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 199,492 control chromosomes in the GnomAD database, including 29 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 0.016 ( 25 hom., cov: 30)
Exomes 𝑓: 0.0096 ( 4 hom. )
Consequence
CXCR2
NM_001557.4 3_prime_UTR
NM_001557.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.789
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]
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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=-0.98).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0159 (2351/147718) while in subpopulation SAS AF= 0.0461 (214/4638). AF 95% confidence interval is 0.0411. There are 25 homozygotes in gnomad4. There are 1177 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 25 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCR2 | NM_001557.4 | c.*355C>T | 3_prime_UTR_variant | 3/3 | ENST00000318507.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR2 | ENST00000318507.7 | c.*355C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_001557.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0159 AC: 2345AN: 147620Hom.: 24 Cov.: 30
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GnomAD4 exome AF: 0.00956 AC: 495AN: 51774Hom.: 4 Cov.: 0 AF XY: 0.0108 AC XY: 279AN XY: 25718
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GnomAD4 genome ? AF: 0.0159 AC: 2351AN: 147718Hom.: 25 Cov.: 30 AF XY: 0.0164 AC XY: 1177AN XY: 71790
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at