chr6-167116814-C-G

Position:

• chr6-167116814-C-G

Variant summary

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

The ENST00000642778.1(ENSG00000284825):​n.473G>C 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 0.161 in 152,348 control chromosomes in the GnomAD database, including 2,921 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 0.16 (2920 hom., cov: 32)
  • Exomes 𝑓: 0.043 (1 hom.)
• Consequence: ENST00000642778.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_004367.6	c.-98+4800C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642778.1	n.473G>C		non_coding_transcript_exon_variant	3/4
CCR6	ENST00000400926.5	c.-98+4800C>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24537 AN: 152138 Hom.: 2903 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.0435 AC: 4 AN: 92 Hom.: 1 Cov.: 0 AF XY: 0.0417 AC XY: 3 AN XY: 72

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0233

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.162 AC: 24597 AN: 152256 Hom.: 2920 Cov.: 32 AF XY: 0.159 AC XY: 11877 AN XY: 74468

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0633

Gnomad4 NFE AF: 0.0855

Gnomad4 OTH AF: 0.158

Alfa AF: 0.126 Hom.: 227

Bravo AF: 0.169

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.80
DANN	Benign	0.19

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: rs6927645; hg19: chr6-167530302;