Genetic Variant CCR6:c.*609G>A (chr6-167137964-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031409.4(CCR6):c.*609G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 153,012 control chromosomes in the GnomAD database, including 856 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 0.088 ( 846 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10 hom. )

Consequence

CCR6
NM_031409.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.157

Publications

10 publications found

Variant links:

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]

CCR6 links:

ENSG00000272980 (HGNC:):

ENSG00000272980 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031409.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCR6	NM_031409.4	MANE Select	c.*609G>A	3_prime_UTR	Exon 3 of 3	NP_113597.2
CCR6	NM_001394582.1		c.*609G>A	3_prime_UTR	Exon 4 of 4	NP_001381511.1
CCR6	NM_004367.6		c.*609G>A	3_prime_UTR	Exon 3 of 3	NP_004358.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCR6	ENST00000341935.10	TSL:1 MANE Select	c.*609G>A	3_prime_UTR	Exon 3 of 3	ENSP00000343952.5
ENSG00000272980	ENST00000705249.1		c.*1687G>A	3_prime_UTR	Exon 13 of 13	ENSP00000516101.1
CCR6	ENST00000349984.6	TSL:1	c.*609G>A	3_prime_UTR	Exon 4 of 4	ENSP00000339393.4

Frequencies

GnomAD3 genomes

AF:

0.0877

AC:

13341

AN:

152146

Hom.:

847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0217

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.0852

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0912

Gnomad FIN

AF:

0.0663

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.110

GnomAD4 exome

AF:

0.118

AC:

AN:

748

Hom.:

Cov.:

AF XY:

0.122

AC XY:

AN XY:

400

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.0510

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.146

AC:

AN:

144

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.132

AC:

AN:

462

Other (OTH)

AF:

0.0455

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0877

AC:

13346

AN:

152264

Hom.:

846

Cov.:

AF XY:

0.0842

AC XY:

6270

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.0216

AC:

898

AN:

41556

American (AMR)

AF:

0.0850

AC:

1301

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

592

AN:

3470

East Asian (EAS)

AF:

0.00135

AC:

AN:

5188

South Asian (SAS)

AF:

0.0934

AC:

450

AN:

4818

European-Finnish (FIN)

AF:

0.0663

AC:

704

AN:

10614

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.131

AC:

8885

AN:

68002

Other (OTH)

AF:

0.109

AC:

230

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

612

1224

1836

2448

3060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.114

Hom.:

1766

Bravo

AF:

0.0875

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.32

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over