rs658559
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002990.5(CCL22):c.*2138G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,296 control chromosomes in the GnomAD database, including 23,939 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 0.53 ( 23885 hom., cov: 32)
Exomes 𝑓: 0.64 ( 54 hom. )
Consequence
CCL22
NM_002990.5 3_prime_UTR
NM_002990.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.236
Genes affected
CCL22 (HGNC:10621): (C-C motif chemokine ligand 22) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 16. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for monocytes, dendritic cells, natural killer cells and for chronically activated T lymphocytes. It also displays a mild activity for primary activated T lymphocytes and has no chemoattractant activity for neutrophils, eosinophils and resting T lymphocytes. The product of this gene binds to chemokine receptor CCR4. This chemokine may play a role in the trafficking of activated T lymphocytes to inflammatory sites and other aspects of activated T lymphocyte physiology. [provided by RefSeq, Sep 2014]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL22 | NM_002990.5 | c.*2138G>A | 3_prime_UTR_variant | 3/3 | ENST00000219235.5 | ||
CCL22 | XM_047434449.1 | c.*2138G>A | 3_prime_UTR_variant | 4/4 | |||
CCL22 | XM_047434450.1 | c.*2138G>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL22 | ENST00000219235.5 | c.*2138G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_002990.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.535 AC: 81292AN: 151918Hom.: 23881 Cov.: 32
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GnomAD4 exome AF: 0.642 AC: 167AN: 260Hom.: 54 Cov.: 0 AF XY: 0.654 AC XY: 123AN XY: 188
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GnomAD4 genome ? AF: 0.535 AC: 81321AN: 152036Hom.: 23885 Cov.: 32 AF XY: 0.534 AC XY: 39723AN XY: 74322
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ClinVar
Not reported inComputational scores
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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