4-73998577-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002994.5(CXCL5):c.5G>A(p.Ser2Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000385 in 1,585,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002994.5 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 |
---|---|---|---|---|---|---|---|
CXCL5 | NM_002994.5 | c.5G>A | p.Ser2Asn | missense_variant | 1/4 | ENST00000296027.5 | |
LOC124900715 | XR_007058140.1 | n.350C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL5 | ENST00000296027.5 | c.5G>A | p.Ser2Asn | missense_variant | 1/4 | 1 | NM_002994.5 | P1 | |
ENST00000669992.1 | n.645C>T | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000350 AC: 7AN: 200188Hom.: 0 AF XY: 0.0000279 AC XY: 3AN XY: 107344
GnomAD4 exome AF: 0.0000377 AC: 54AN: 1432922Hom.: 0 Cov.: 33 AF XY: 0.0000422 AC XY: 30AN XY: 710210
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.5G>A (p.S2N) alteration is located in exon 1 (coding exon 1) of the CXCL5 gene. This alteration results from a G to A substitution at nucleotide position 5, causing the serine (S) at amino acid position 2 to be replaced by an asparagine (N). 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