chr6-167135059-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031409.4(CCR6):c.-97-979A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0704 in 152,340 control chromosomes in the GnomAD database, including 509 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 0.070 ( 508 hom., cov: 33)
Exomes 𝑓: 0.076 ( 1 hom. )
Consequence
CCR6
NM_031409.4 intron
NM_031409.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0620
Publications
7 publications found
Genes affected
CCR6 (HGNC:1607): (C-C motif chemokine receptor 6) This gene encodes a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. The gene is preferentially expressed by immature dendritic cells and memory T cells. The ligand of this receptor is macrophage inflammatory protein 3 alpha (MIP-3 alpha). This receptor has been shown to be important for B-lineage maturation and antigen-driven B-cell differentiation, and it may regulate the migration and recruitment of dentritic and T cells during inflammatory and immunological responses. Alternatively spliced transcript variants that encode the same protein have been described for this gene. [provided by RefSeq, Jul 2008]
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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=-0.78).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCR6 | NM_031409.4 | c.-97-979A>G | intron_variant | Intron 1 of 2 | ENST00000341935.10 | NP_113597.2 | ||
CCR6 | NM_001394582.1 | c.-97-979A>G | intron_variant | Intron 2 of 3 | NP_001381511.1 | |||
CCR6 | NM_004367.6 | c.-97-979A>G | intron_variant | Intron 1 of 2 | NP_004358.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCR6 | ENST00000341935.10 | c.-97-979A>G | intron_variant | Intron 1 of 2 | 1 | NM_031409.4 | ENSP00000343952.5 | |||
ENSG00000272980 | ENST00000705249.1 | c.1066-979A>G | intron_variant | Intron 11 of 12 | ENSP00000516101.1 |
Frequencies
GnomAD3 genomes AF: 0.0704 AC: 10713AN: 152104Hom.: 509 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
10713
AN:
152104
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.0763 AC: 9AN: 118Hom.: 1 Cov.: 0 AF XY: 0.0816 AC XY: 8AN XY: 98 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
118
Hom.:
Cov.:
0
AF XY:
AC XY:
8
AN XY:
98
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
4
East Asian (EAS)
AF:
AC:
0
AN:
4
South Asian (SAS)
AF:
AC:
0
AN:
2
European-Finnish (FIN)
AF:
AC:
1
AN:
4
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
6
AN:
96
Other (OTH)
AF:
AC:
1
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.404
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0704 AC: 10714AN: 152222Hom.: 508 Cov.: 33 AF XY: 0.0730 AC XY: 5431AN XY: 74420 show subpopulations
GnomAD4 genome
AF:
AC:
10714
AN:
152222
Hom.:
Cov.:
33
AF XY:
AC XY:
5431
AN XY:
74420
show subpopulations
African (AFR)
AF:
AC:
660
AN:
41546
American (AMR)
AF:
AC:
1568
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
220
AN:
3472
East Asian (EAS)
AF:
AC:
358
AN:
5176
South Asian (SAS)
AF:
AC:
361
AN:
4816
European-Finnish (FIN)
AF:
AC:
1430
AN:
10592
Middle Eastern (MID)
AF:
AC:
12
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5958
AN:
68010
Other (OTH)
AF:
AC:
114
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
512
1024
1535
2047
2559
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
118
236
354
472
590
<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:
200
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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