17-34320363-C-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005623.3(CCL8):c.171C>A(p.Ile57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,611,714 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0077 ( 17 hom., cov: 32)
Exomes 𝑓: 0.00076 ( 16 hom. )
Consequence
CCL8
NM_005623.3 synonymous
NM_005623.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.424
Genes affected
CCL8 (HGNC:10635): (C-C motif chemokine ligand 8) This antimicrobial gene is one of several chemokine genes clustered on the q-arm of chromosome 17. Chemokines form a superfamily of secreted proteins involved in immunoregulatory and inflammatory processes. The superfamily is divided into four subfamilies based on the arrangement of N-terminal cysteine residues of the mature peptide. This chemokine is a member of the CC subfamily which is characterized by two adjacent cysteine residues. This cytokine displays chemotactic activity for monocytes, lymphocytes, basophils and eosinophils. By recruiting leukocytes to sites of inflammation this cytokine may contribute to tumor-associated leukocyte infiltration and to the antiviral state against HIV infection. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 17-34320363-C-A is Benign according to our data. Variant chr17-34320363-C-A is described in ClinVar as [Benign]. Clinvar id is 780421.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00771 (1175/152322) while in subpopulation AFR AF= 0.0264 (1098/41574). AF 95% confidence interval is 0.0251. There are 17 homozygotes in gnomad4. There are 516 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL8 | NM_005623.3 | c.171C>A | p.Ile57= | synonymous_variant | 2/3 | ENST00000394620.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL8 | ENST00000394620.2 | c.171C>A | p.Ile57= | synonymous_variant | 2/3 | 1 | NM_005623.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00772 AC: 1175AN: 152204Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.00204 AC: 511AN: 250850Hom.: 8 AF XY: 0.00154 AC XY: 209AN XY: 135550
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GnomAD4 exome AF: 0.000755 AC: 1102AN: 1459392Hom.: 16 Cov.: 30 AF XY: 0.000646 AC XY: 469AN XY: 726188
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GnomAD4 genome ? AF: 0.00771 AC: 1175AN: 152322Hom.: 17 Cov.: 32 AF XY: 0.00693 AC XY: 516AN XY: 74478
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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 | Apr 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at