chr4-74099033-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002089.4(CXCL2):c.88C>T(p.Arg30Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000272 in 1,472,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R30G) has been classified as Uncertain significance.
Frequency
Consequence
NM_002089.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL2 | NM_002089.4 | c.88C>T | p.Arg30Trp | missense_variant | 1/4 | ENST00000508487.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL2 | ENST00000508487.3 | c.88C>T | p.Arg30Trp | missense_variant | 1/4 | 1 | NM_002089.4 | P1 | |
CXCL2 | ENST00000296031.4 | n.163C>T | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
CXCL2 | ENST00000510048.1 | n.164C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 2AN: 71580Hom.: 0 AF XY: 0.0000252 AC XY: 1AN XY: 39656
GnomAD4 exome AF: 0.00000227 AC: 3AN: 1320860Hom.: 0 Cov.: 30 AF XY: 0.00000462 AC XY: 3AN XY: 649610
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.88C>T (p.R30W) alteration is located in exon 1 (coding exon 1) of the CXCL2 gene. This alteration results from a C to T substitution at nucleotide position 88, causing the arginine (R) at amino acid position 30 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at