rs3093005

Variant names:

• chr6-167138185-T-C
• rs3093005
• NM_031409.4:c.*830T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031409.4(CCR6):​c.*830T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,404 control chromosomes in the GnomAD database, including 95 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 0.031 (95 hom., cov: 33)
  • Exomes 𝑓: 0.031 (0 hom.)
• Consequence: CCR6 NM_031409.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR6	NM_031409.4	c.*830T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000341935.10	NP_113597.2
CCR6	NM_001394582.1	c.*830T>C		3_prime_UTR_variant	Exon 4 of 4		NP_001381511.1
CCR6	NM_004367.6	c.*830T>C		3_prime_UTR_variant	Exon 3 of 3		NP_004358.2
LOC112267970	XR_002956379.2	n.*124A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10	c.*830T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_031409.4	ENSP00000343952.5
ENSG00000272980	ENST00000705249.1	c.*1908T>C		3_prime_UTR_variant	Exon 13 of 13			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4657 AN: 152158 Hom.: 94 Cov.: 33

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0663

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0350

GnomAD4 exome AF: 0.0313 AC: 4 AN: 128 Hom.: 0 Cov.: 0 AF XY: 0.0294 AC XY: 2 AN XY: 68

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0328 AC: 4 AN: 122

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) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0307 AC: 4672 AN: 152276 Hom.: 95 Cov.: 33 AF XY: 0.0310 AC XY: 2309 AN XY: 74482

African (AFR) AF: 0.0467 AC: 1940 AN: 41554

American (AMR) AF: 0.0280 AC: 429 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.0663 AC: 344 AN: 5188

South Asian (SAS) AF: 0.0372 AC: 179 AN: 4814

European-Finnish (FIN) AF: 0.0104 AC: 110 AN: 10624

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

European-Non Finnish (NFE) AF: 0.0210 AC: 1429 AN: 68012

Other (OTH) AF: 0.0346 AC: 73 AN: 2110

Alfa AF: 0.0241 Hom.: 128

Bravo AF: 0.0332

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.31
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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: rs3093005; hg19: chr6-167551673;