6-167138185-T-C

Position:

• chr6-167138185-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CCR6	NM_031409.4	c.*830T>C		3_prime_UTR_variant	3/3	ENST00000341935.10	NP_113597.2
CCR6	NM_001394582.1	c.*830T>C		3_prime_UTR_variant	4/4		NP_001381511.1
CCR6	NM_004367.6	c.*830T>C		3_prime_UTR_variant	3/3		NP_004358.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10	c.*830T>C		3_prime_UTR_variant	3/3	1	NM_031409.4	ENSP00000343952.5
ENSG00000272980	ENST00000705249.1	c.*1908T>C		3_prime_UTR_variant	13/13			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

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.0328

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0663

Gnomad4 SAS AF: 0.0372

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0244 Hom.: 55

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

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: rs3093005; hg19: chr6-167551673;