6-167118883-T-G

Position:

• chr6-167118883-T-G

Variant summary

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

The NM_004367.6(CCR6):​c.-98+6869T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,124 control chromosomes in the GnomAD database, including 4,401 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 0.19 (4401 hom., cov: 32)
• Consequence: CCR6 NM_004367.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

Genes affected

ENSG00000272980 (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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR6	NM_004367.6	c.-98+6869T>G		intron_variant			NP_004358.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272980	ENST00000705249.1	c.1066-17155T>G		intron_variant				ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28526 AN: 152006 Hom.: 4389 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.177

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.188 AC: 28579 AN: 152124 Hom.: 4401 Cov.: 32 AF XY: 0.184 AC XY: 13706 AN XY: 74384

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.177

Alfa AF: 0.104 Hom.: 366

Bravo AF: 0.200

Asia WGS AF: 0.231 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.35

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: rs3093027; hg19: chr6-167532371;