rs45606837
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001557.4(CXCR2):c.936C>T(p.Leu312=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,614,158 control chromosomes in the GnomAD database, including 217 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 16 hom., cov: 31)
Exomes 𝑓: 0.013 ( 201 hom. )
Consequence
CXCR2
NM_001557.4 synonymous
NM_001557.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.595
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 2-218135737-C-T is Benign according to our data. Variant chr2-218135737-C-T is described in ClinVar as [Benign]. Clinvar id is 1164697.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.595 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0102 (1558/152270) while in subpopulation SAS AF= 0.0384 (185/4816). AF 95% confidence interval is 0.0339. There are 16 homozygotes in gnomad4. There are 852 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 16 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCR2 | NM_001557.4 | c.936C>T | p.Leu312= | synonymous_variant | 3/3 | ENST00000318507.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR2 | ENST00000318507.7 | c.936C>T | p.Leu312= | synonymous_variant | 3/3 | 1 | NM_001557.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1560AN: 152152Hom.: 17 Cov.: 31
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GnomAD3 exomes AF: 0.0137 AC: 3434AN: 251476Hom.: 51 AF XY: 0.0156 AC XY: 2118AN XY: 135912
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GnomAD4 exome AF: 0.0126 AC: 18440AN: 1461888Hom.: 201 Cov.: 34 AF XY: 0.0135 AC XY: 9847AN XY: 727246
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GnomAD4 genome ? AF: 0.0102 AC: 1558AN: 152270Hom.: 16 Cov.: 31 AF XY: 0.0114 AC XY: 852AN XY: 74460
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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 | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at