rs3093026

Positions:

• chr6-167119202-C-T

Variant summary

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

The ENST00000642778.1(ENSG00000284825):​n.183G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,190 control chromosomes in the GnomAD database, including 14,969 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 0.44 (14946 hom., cov: 32)
  • Exomes 𝑓: 0.46 (23 hom.)
• Consequence: ENST00000642778.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

Genes affected

(HGNC:):

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_004367.6	c.-98+7188C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642778.1	n.183G>A		non_coding_transcript_exon_variant	2/4
CCR6	ENST00000400926.5	c.-98+7188C>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66148 AN: 151862 Hom.: 14922 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.454

GnomAD4 exome AF: 0.458 AC: 97 AN: 212 Hom.: 23 Cov.: 0 AF XY: 0.444 AC XY: 48 AN XY: 108

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.548

Gnomad4 NFE exome AF: 0.435

Gnomad4 OTH exome AF: 0.313

GnomAD4 genome AF: 0.436 AC: 66221 AN: 151978 Hom.: 14946 Cov.: 32 AF XY: 0.435 AC XY: 32331 AN XY: 74274

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.460

Alfa AF: 0.453 Hom.: 2830

Bravo AF: 0.439

Asia WGS AF: 0.407 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.33

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: rs3093026; hg19: chr6-167532690; COSMIC: COSV59476011; COSMIC: COSV59476011;