Variant chr6-167136287-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000341935.10(CCR6):c.57T>C(p.Phe19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,608,874 control chromosomes in the GnomAD database, including 25,769 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 0.17 ( 2240 hom., cov: 33)

Exomes 𝑓: 0.18 ( 23529 hom. )

Consequence

CCR6
ENST00000341935.10 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=-2.19 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CCR6	NM_031409.4 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	3/3	ENST00000341935.10	NP_113597.2
CCR6	NM_001394582.1 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	4/4		NP_001381511.1
CCR6	NM_004367.6 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	3/3		NP_004358.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CCR6	ENST00000341935.10 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	3/3	1	NM_031409.4	ENSP00000343952	P1
CCR6	ENST00000349984.6 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	4/4	1		ENSP00000339393	P1
CCR6	ENST00000400926.5 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	3/3	2		ENSP00000383715	P1
CCR6	ENST00000643861.1 linkuse as main transcript	c.57T>C	p.Phe19=	synonymous_variant	4/4			ENSP00000493637	P1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25378

AN:

152126

Hom.:

2239

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.0580

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.180

GnomAD3 exomes

AF:

0.151

AC:

37231

AN:

246358

Hom.:

3118

AF XY:

0.152

AC XY:

20160

AN XY:

133004

show subpopulations

Gnomad AFR exome

AF:

0.176

Gnomad AMR exome

AF:

0.126

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.0414

Gnomad SAS exome

AF:

0.127

Gnomad FIN exome

AF:

0.133

Gnomad NFE exome

AF:

0.183

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.176

AC:

256951

AN:

1456630

Hom.:

23529

Cov.:

AF XY:

0.175

AC XY:

126896

AN XY:

724166

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.128

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.0799

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.189

Gnomad4 OTH exome

AF:

0.165

GnomAD4 genome

AF:

0.167

AC:

25410

AN:

152244

Hom.:

2240

Cov.:

AF XY:

0.162

AC XY:

12053

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.177

Gnomad4 AMR

AF:

0.147

Gnomad4 ASJ

AF:

0.139

Gnomad4 EAS

AF:

0.0580

Gnomad4 SAS

AF:

0.119

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.185

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.179

Hom.:

4374

Bravo

AF:

0.166

Asia WGS

AF:

0.104

AC:

361

AN:

3478

EpiCase

AF:

0.177

EpiControl

AF:

0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.13

DANN

Benign

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over