rs2302009
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001371938.1(CCL26):c.*13T>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 0.252 in 1,581,242 control chromosomes in the GnomAD database, including 52,309 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 0.29 ( 6810 hom., cov: 32)
Exomes 𝑓: 0.25 ( 45499 hom. )
Consequence
CCL26
NM_001371938.1 3_prime_UTR
NM_001371938.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.696
Genes affected
CCL26 (HGNC:10625): (C-C motif chemokine ligand 26) This gene is one of two Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 7. 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 normal peripheral blood eosinophils and basophils. This protein also has antimicrobial activity, displaying an antibacterial effect on S. pneumoniae, S. aureus, Non-typeable H. influenzae, and P. aeruginosa. The product of this gene is one of three related chemokines that specifically activate chemokine receptor CCR3. This chemokine may contribute to the eosinophil accumulation in atopic diseases. [provided by RefSeq, Jul 2020]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL26 | NM_001371938.1 | c.*13T>G | 3_prime_UTR_variant | 3/3 | ENST00000005180.9 | ||
CCL26 | NM_001371936.1 | c.*13T>G | 3_prime_UTR_variant | 4/4 | |||
CCL26 | NM_006072.4 | c.*13T>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL26 | ENST00000005180.9 | c.*13T>G | 3_prime_UTR_variant | 3/3 | 1 | NM_001371938.1 | P1 | ||
CCL26 | ENST00000394905.2 | c.*13T>G | 3_prime_UTR_variant | 4/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.288 AC: 43720AN: 152044Hom.: 6796 Cov.: 32
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GnomAD3 exomes AF: 0.244 AC: 61138AN: 250758Hom.: 7958 AF XY: 0.241 AC XY: 32659AN XY: 135558
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GnomAD4 exome AF: 0.248 AC: 354880AN: 1429080Hom.: 45499 Cov.: 25 AF XY: 0.247 AC XY: 176312AN XY: 713004
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GnomAD4 genome ? AF: 0.288 AC: 43772AN: 152162Hom.: 6810 Cov.: 32 AF XY: 0.285 AC XY: 21181AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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