dbSNP rs3093006: 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:

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=-0.9).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCR6	NM_031409.4 link	c.*609G>A	3_prime_UTR_variant	Exon 3 of 3	ENST00000341935.10	NP_113597.2	P51684
CCR6	NM_001394582.1 link	c.*609G>A	3_prime_UTR_variant	Exon 4 of 4		NP_001381511.1
CCR6	NM_004367.6 link	c.*609G>A	3_prime_UTR_variant	Exon 3 of 3		NP_004358.2	P51684

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10 link	c.*609G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_031409.4	ENSP00000343952.5		P51684
ENSG00000272980	ENST00000705249.1 link	c.*1687G>A		3_prime_UTR_variant	Exon 13 of 13			ENSP00000516101.1		A0A994J5H4

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over