rs3093006

chr6-167137964-G-Achr6-167137964-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_031409.4	c.*609G>A		3_prime_UTR_variant	3/3	ENST00000341935.10
CCR6	NM_001394582.1	c.*609G>A		3_prime_UTR_variant	4/4
CCR6	NM_004367.6	c.*609G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR6	ENST00000341935.10	c.*609G>A		3_prime_UTR_variant	3/3	1	NM_031409.4	P1
CCR6	ENST00000349984.6	c.*609G>A		3_prime_UTR_variant	4/4	1		P1
CCR6	ENST00000400926.5	c.*609G>A		3_prime_UTR_variant	3/3	2		P1

Frequencies

GnomAD3 genomes AF: 0.0877 AC: 13341 AN: 152146 Hom.: 847 Cov.: 32

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: 88 AN: 748 Hom.: 10 Cov.: 0 AF XY: 0.122 AC XY: 49 AN XY: 400

Gnomad4 AMR exome AF: 0.0510

Gnomad4 EAS exome AF: 0.146

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.0455

GnomAD4 genome AF: 0.0877 AC: 13346 AN: 152264 Hom.: 846 Cov.: 32 AF XY: 0.0842 AC XY: 6270 AN XY: 74464

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.109

Alfa AF: 0.119 Hom.: 1261

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
Dann	Benign	0.32

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

LitVar

Other links and lift over

dbSNP: rs3093006; hg19: chr6-167551452;