rs1126579
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001557.4(CXCR2):c.*127T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,294,684 control chromosomes in the GnomAD database, including 197,452 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.61 ( 30342 hom., cov: 30)
Exomes 𝑓: 0.54 ( 167110 hom. )
Consequence
CXCR2
NM_001557.4 3_prime_UTR
NM_001557.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.752
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 2-218136011-T-C is Benign according to our data. Variant chr2-218136011-T-C is described in ClinVar as [Benign]. Clinvar id is 1222897.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCR2 | NM_001557.4 | c.*127T>C | 3_prime_UTR_variant | 3/3 | ENST00000318507.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR2 | ENST00000318507.7 | c.*127T>C | 3_prime_UTR_variant | 3/3 | 1 | NM_001557.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.614 AC: 93167AN: 151812Hom.: 30290 Cov.: 30
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GnomAD4 exome AF: 0.537 AC: 614201AN: 1142754Hom.: 167110 Cov.: 16 AF XY: 0.538 AC XY: 305393AN XY: 567228
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GnomAD4 genome ? AF: 0.614 AC: 93264AN: 151930Hom.: 30342 Cov.: 30 AF XY: 0.609 AC XY: 45220AN XY: 74264
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | This variant is associated with the following publications: (PMID: 23615182, 25480945) - |
Computational scores
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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