rs11575083

Variant names:

• chr6-167138625-C-T
• rs11575083
• NM_031409.4:c.*1270C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_031409.4(CCR6):​c.*1270C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 152,244 control chromosomes in the GnomAD database, including 21 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 0.016 (21 hom., cov: 31)
  • Exomes 𝑓: 0.029 (0 hom.)
• Consequence: CCR6 NM_031409.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0162 (2465/152106) while in subpopulation AFR AF = 0.0188 (781/41472). AF 95% confidence interval is 0.0177. There are 21 homozygotes in GnomAd4. There are 1180 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 21 AR gene

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.*1270C>T		3_prime_UTR	Exon 3 of 3	NP_113597.2
	CCR6	NM_001394582.1		c.*1270C>T		3_prime_UTR	Exon 4 of 4	NP_001381511.1
	CCR6	NM_004367.6		c.*1270C>T		3_prime_UTR	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.*1270C>T		3_prime_UTR	Exon 3 of 3	ENSP00000343952.5
	ENSG00000272980	ENST00000705249.1		c.*2348C>T		3_prime_UTR	Exon 13 of 13	ENSP00000516101.1
	CCR6	ENST00000349984.6	TSL:1	c.*1270C>T		3_prime_UTR	Exon 4 of 4	ENSP00000339393.4

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 2454 AN: 151988 Hom.: 20 Cov.: 31

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.00910

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0211

GnomAD4 exome AF: 0.0290 AC: 4 AN: 138 Hom.: 0 Cov.: 0 AF XY: 0.0135 AC XY: 1 AN XY: 74

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0294 AC: 4 AN: 136

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0162 AC: 2465 AN: 152106 Hom.: 21 Cov.: 31 AF XY: 0.0159 AC XY: 1180 AN XY: 74368

African (AFR) AF: 0.0188 AC: 781 AN: 41472

American (AMR) AF: 0.0125 AC: 191 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4830

European-Finnish (FIN) AF: 0.00910 AC: 96 AN: 10550

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0177 AC: 1206 AN: 68004

Other (OTH) AF: 0.0209 AC: 44 AN: 2106

Alfa AF: 0.0181 Hom.: 12

Bravo AF: 0.0166

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.56
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs11575083; hg19: chr6-167552113;