rs35795399
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001565.4(CXCL10):c.*406A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 172,580 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.014 ( 29 hom., cov: 33)
Exomes 𝑓: 0.017 ( 5 hom. )
Consequence
CXCL10
NM_001565.4 3_prime_UTR
NM_001565.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.546
Genes affected
CXCL10 (HGNC:10637): (C-X-C motif chemokine ligand 10) This antimicrobial gene encodes a chemokine of the CXC subfamily and ligand for the receptor CXCR3. Binding of this protein to CXCR3 results in pleiotropic effects, including stimulation of monocytes, natural killer and T-cell migration, and modulation of adhesion molecule expression. This gene may also be a key regulator of the 'cytokine storm' immune response to SARS-CoV-2 infection. [provided by RefSeq, Sep 2020]
ART3 (HGNC:725): (ADP-ribosyltransferase 3 (inactive)) This gene encodes an arginine-specific ADP-ribosyltransferase. The encoded protein catalyzes a reversible reaction which modifies proteins by the addition or removal of ADP-ribose to an arginine residue to regulate the function of the modified protein. An ADP-ribosyltransferase pseudogene is located on chromosome 11. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0145 (2202/152330) while in subpopulation NFE AF= 0.0222 (1510/68034). AF 95% confidence interval is 0.0213. There are 29 homozygotes in gnomad4. There are 1068 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2203 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL10 | NM_001565.4 | c.*406A>G | 3_prime_UTR_variant | 4/4 | ENST00000306602.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL10 | ENST00000306602.3 | c.*406A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_001565.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0145 AC: 2203AN: 152212Hom.: 29 Cov.: 33
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GnomAD4 exome AF: 0.0174 AC: 352AN: 20250Hom.: 5 Cov.: 0 AF XY: 0.0168 AC XY: 175AN XY: 10418
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GnomAD4 genome ? AF: 0.0145 AC: 2202AN: 152330Hom.: 29 Cov.: 33 AF XY: 0.0143 AC XY: 1068AN XY: 74488
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at