rs3093007

Variant names:

• chr6-167136287-T-C
• rs3093007
• NM_031409.4:c.57T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_031409.4(CCR6):​c.57T>C​(p.Phe19Phe) 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 NM_031409.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 20 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]

ENSG00000272980 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR6	NM_031409.4	MANE Select	c.57T>C	p.Phe19Phe	synonymous	Exon 3 of 3	NP_113597.2
	CCR6	NM_001394582.1		c.57T>C	p.Phe19Phe	synonymous	Exon 4 of 4	NP_001381511.1
	CCR6	NM_004367.6		c.57T>C	p.Phe19Phe	synonymous	Exon 3 of 3	NP_004358.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR6	ENST00000341935.10	TSL:1 MANE Select	c.57T>C	p.Phe19Phe	synonymous	Exon 3 of 3	ENSP00000343952.5
	CCR6	ENST00000349984.6	TSL:1	c.57T>C	p.Phe19Phe	synonymous	Exon 4 of 4	ENSP00000339393.4
	ENSG00000272980	ENST00000705249.1		c.*10T>C		3_prime_UTR	Exon 13 of 13	ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25378 AN: 152126 Hom.: 2239 Cov.: 33

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

GnomAD2 exomes AF: 0.151 AC: 37231 AN: 246358 AF XY: 0.152

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 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.: 34 AF XY: 0.175 AC XY: 126896 AN XY: 724166

African (AFR) AF: 0.173 AC: 5741 AN: 33220

American (AMR) AF: 0.128 AC: 5586 AN: 43688

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 3617 AN: 25904

East Asian (EAS) AF: 0.0799 AC: 3165 AN: 39636

South Asian (SAS) AF: 0.122 AC: 10393 AN: 84930

European-Finnish (FIN) AF: 0.139 AC: 7419 AN: 53340

Middle Eastern (MID) AF: 0.135 AC: 778 AN: 5752

European-Non Finnish (NFE) AF: 0.189 AC: 210330 AN: 1109936

Other (OTH) AF: 0.165 AC: 9922 AN: 60224

GnomAD4 genome AF: 0.167 AC: 25410 AN: 152244 Hom.: 2240 Cov.: 33 AF XY: 0.162 AC XY: 12053 AN XY: 74438

African (AFR) AF: 0.177 AC: 7359 AN: 41546

American (AMR) AF: 0.147 AC: 2246 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3468

East Asian (EAS) AF: 0.0580 AC: 300 AN: 5176

South Asian (SAS) AF: 0.119 AC: 573 AN: 4830

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10600

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12584 AN: 68006

Other (OTH) AF: 0.180 AC: 381 AN: 2112

Alfa AF: 0.179 Hom.: 6264

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.13
DANN	Benign	0.52
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3093007; hg19: chr6-167549775; COSMIC: COSV59474327; COSMIC: COSV59474327;