4-74038389-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_002090.3(CXCL3):c.125G>A(p.Arg42His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,461,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002090.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CXCL3 | ENST00000296026.4 | c.125G>A | p.Arg42His | missense_variant | Exon 2 of 4 | 1 | NM_002090.3 | ENSP00000296026.4 | ||
CXCL3 | ENST00000511669.1 | n.321G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
CXCL3 | ENST00000502974.1 | n.301G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | |||||
CXCL3 | ENST00000510390.1 | n.164G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727208
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.125G>A (p.R42H) alteration is located in exon 2 (coding exon 2) of the CXCL3 gene. This alteration results from a G to A substitution at nucleotide position 125, causing the arginine (R) at amino acid position 42 to be replaced by a histidine (H). 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