chr7-75769680-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001371938.1(CCL26):c.*13T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
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
Publications
30 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCL26 | NM_001371938.1 | c.*13T>A | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000005180.9 | NP_001358867.1 | ||
CCL26 | NM_001371936.1 | c.*13T>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001358865.1 | |||
CCL26 | NM_006072.4 | c.*13T>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_006063.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1431256Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 713970
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1431256
Hom.:
Cov.:
25
AF XY:
AC XY:
0
AN XY:
713970
African (AFR)
AF:
AC:
0
AN:
32868
American (AMR)
AF:
AC:
0
AN:
44656
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25930
East Asian (EAS)
AF:
AC:
0
AN:
39518
South Asian (SAS)
AF:
AC:
0
AN:
85648
European-Finnish (FIN)
AF:
AC:
0
AN:
53384
Middle Eastern (MID)
AF:
AC:
0
AN:
5714
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1084262
Other (OTH)
AF:
AC:
0
AN:
59276
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.