chr4-76022401-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001565.4(CXCL10):c.243C>A(p.Ala81=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000975 in 1,613,576 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0052 ( 8 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 9 hom. )
Consequence
CXCL10
NM_001565.4 synonymous
NM_001565.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.290
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 4-76022401-G-T is Benign according to our data. Variant chr4-76022401-G-T is described in ClinVar as [Benign]. Clinvar id is 731714.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.29 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00517 (787/152252) while in subpopulation AFR AF= 0.0176 (730/41544). AF 95% confidence interval is 0.0165. There are 8 homozygotes in gnomad4. There are 357 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 789 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL10 | NM_001565.4 | c.243C>A | p.Ala81= | synonymous_variant | 3/4 | ENST00000306602.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL10 | ENST00000306602.3 | c.243C>A | p.Ala81= | synonymous_variant | 3/4 | 1 | NM_001565.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00519 AC: 789AN: 152134Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00144 AC: 358AN: 249214Hom.: 5 AF XY: 0.00105 AC XY: 142AN XY: 135244
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GnomAD4 exome AF: 0.000539 AC: 787AN: 1461324Hom.: 9 Cov.: 31 AF XY: 0.000469 AC XY: 341AN XY: 726968
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at