chr7-75769680-A-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
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: Benign. The variant received -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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCL26 | NM_001371938.1 | c.*13T>G | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000005180.9 | NP_001358867.1 | ||
CCL26 | NM_001371936.1 | c.*13T>G | 3_prime_UTR_variant | Exon 4 of 4 | NP_001358865.1 | |||
CCL26 | NM_006072.4 | c.*13T>G | 3_prime_UTR_variant | Exon 4 of 4 | NP_006063.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.288 AC: 43720AN: 152044Hom.: 6796 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
43720
AN:
152044
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.244 AC: 61138AN: 250758 AF XY: 0.241 show subpopulations
GnomAD2 exomes
AF:
AC:
61138
AN:
250758
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.248 AC: 354880AN: 1429080Hom.: 45499 Cov.: 25 AF XY: 0.247 AC XY: 176312AN XY: 713004 show subpopulations
GnomAD4 exome
AF:
AC:
354880
AN:
1429080
Hom.:
Cov.:
25
AF XY:
AC XY:
176312
AN XY:
713004
show subpopulations
African (AFR)
AF:
AC:
13472
AN:
32832
American (AMR)
AF:
AC:
8744
AN:
44650
Ashkenazi Jewish (ASJ)
AF:
AC:
6475
AN:
25902
East Asian (EAS)
AF:
AC:
4086
AN:
39512
South Asian (SAS)
AF:
AC:
19125
AN:
85600
European-Finnish (FIN)
AF:
AC:
15852
AN:
53364
Middle Eastern (MID)
AF:
AC:
1289
AN:
5710
European-Non Finnish (NFE)
AF:
AC:
270836
AN:
1082310
Other (OTH)
AF:
AC:
15001
AN:
59200
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
12425
24849
37274
49698
62123
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
9026
18052
27078
36104
45130
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.288 AC: 43772AN: 152162Hom.: 6810 Cov.: 32 AF XY: 0.285 AC XY: 21181AN XY: 74378 show subpopulations
GnomAD4 genome
AF:
AC:
43772
AN:
152162
Hom.:
Cov.:
32
AF XY:
AC XY:
21181
AN XY:
74378
show subpopulations
African (AFR)
AF:
AC:
16649
AN:
41508
American (AMR)
AF:
AC:
3604
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
857
AN:
3472
East Asian (EAS)
AF:
AC:
598
AN:
5182
South Asian (SAS)
AF:
AC:
1014
AN:
4826
European-Finnish (FIN)
AF:
AC:
3067
AN:
10590
Middle Eastern (MID)
AF:
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
AC:
17115
AN:
67996
Other (OTH)
AF:
AC:
567
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1611
3222
4833
6444
8055
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
430
860
1290
1720
2150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
611
AN:
3478
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
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