rs3093012

Positions:

• chr6-167134793-A-G
• chr6-167134793-A-T

Variant summary

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

The NM_031409.4(CCR6):​c.-97-1245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,158 control chromosomes in the GnomAD database, including 22,035 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 0.53 (22030 hom., cov: 33)
  • Exomes 𝑓: 0.50 (5 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_031409.4	c.-97-1245A>G		intron_variant		ENST00000341935.10
CCR6	NM_001394582.1	c.-97-1245A>G		intron_variant
CCR6	NM_004367.6	c.-97-1245A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR6	ENST00000341935.10	c.-97-1245A>G		intron_variant		1	NM_031409.4	P1
CCR6	ENST00000349984.6	c.-97-1245A>G		intron_variant		1		P1
CCR6	ENST00000400926.5	c.-97-1245A>G		intron_variant		2		P1
CCR6	ENST00000643861.1	c.-97-1245A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80668 AN: 152000 Hom.: 22011 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.510

GnomAD4 exome AF: 0.500 AC: 20 AN: 40 Hom.: 5 AF XY: 0.429 AC XY: 12 AN XY: 28

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.531 AC: 80741 AN: 152118 Hom.: 22030 Cov.: 33 AF XY: 0.534 AC XY: 39698 AN XY: 74386

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.514

Alfa AF: 0.572 Hom.: 29374

Bravo AF: 0.528

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.18

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: rs3093012; hg19: chr6-167548281;