rs2240478
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001371938.1(CCL26):c.73+4C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,586,878 control chromosomes in the GnomAD database, including 33,940 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 0.21 ( 3664 hom., cov: 32)
Exomes 𝑓: 0.20 ( 30276 hom. )
Consequence
CCL26
NM_001371938.1 splice_donor_region, intron
NM_001371938.1 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0007954
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.912
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=-0.78).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL26 | NM_001371938.1 | c.73+4C>T | splice_donor_region_variant, intron_variant | ENST00000005180.9 | |||
CCL26 | NM_001371936.1 | c.73+4C>T | splice_donor_region_variant, intron_variant | ||||
CCL26 | NM_006072.4 | c.73+4C>T | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL26 | ENST00000005180.9 | c.73+4C>T | splice_donor_region_variant, intron_variant | 1 | NM_001371938.1 | P1 | |||
CCL26 | ENST00000394905.2 | c.73+4C>T | splice_donor_region_variant, intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.209 AC: 31757AN: 152010Hom.: 3651 Cov.: 32
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GnomAD3 exomes AF: 0.234 AC: 48317AN: 206616Hom.: 6736 AF XY: 0.225 AC XY: 24978AN XY: 111068
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GnomAD4 exome AF: 0.197 AC: 283362AN: 1434750Hom.: 30276 Cov.: 31 AF XY: 0.196 AC XY: 139735AN XY: 711840
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GnomAD4 genome ? AF: 0.209 AC: 31787AN: 152128Hom.: 3664 Cov.: 32 AF XY: 0.212 AC XY: 15793AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at