chr4-74038562-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002090.3(CXCL3):c.50G>T(p.Arg17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000671 in 1,490,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002090.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CXCL3 | ENST00000296026.4 | c.50G>T | p.Arg17Leu | missense_variant | Exon 1 of 4 | 1 | NM_002090.3 | ENSP00000296026.4 | ||
CXCL3 | ENST00000511669.1 | n.246G>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
CXCL3 | ENST00000502974.1 | n.128G>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | |||||
CXCL3 | ENST00000510390.1 | n.89G>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000448 AC: 6AN: 1338304Hom.: 0 Cov.: 30 AF XY: 0.00000304 AC XY: 2AN XY: 658948
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.50G>T (p.R17L) alteration is located in exon 1 (coding exon 1) of the CXCL3 gene. This alteration results from a G to T substitution at nucleotide position 50, causing the arginine (R) at amino acid position 17 to be replaced by a leucine (L). 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