rs2234671
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000634.3(CXCR1):c.827G>C(p.Ser276Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 1,613,424 control chromosomes in the GnomAD database, including 5,617 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000634.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCR1 | NM_000634.3 | c.827G>C | p.Ser276Thr | missense_variant | 2/2 | ENST00000295683.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR1 | ENST00000295683.3 | c.827G>C | p.Ser276Thr | missense_variant | 2/2 | 1 | NM_000634.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.107 AC: 16191AN: 151972Hom.: 1222 Cov.: 32
GnomAD3 exomes AF: 0.0910 AC: 22808AN: 250754Hom.: 1451 AF XY: 0.0883 AC XY: 11965AN XY: 135506
GnomAD4 exome AF: 0.0683 AC: 99797AN: 1461334Hom.: 4389 Cov.: 32 AF XY: 0.0694 AC XY: 50420AN XY: 726914
GnomAD4 genome ? AF: 0.107 AC: 16214AN: 152090Hom.: 1228 Cov.: 32 AF XY: 0.109 AC XY: 8075AN XY: 74356
ClinVar
Submissions by phenotype
CXCR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cholangiocarcinoma Other:1
other, no assertion criteria provided | research | Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin | Dec 10, 2022 | No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at