6-167131221-C-T

Variant summary

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

The NM_031409.4(CCR6):c.-97-4817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 152,294 control chromosomes in the GnomAD database, including 847 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 0.099 (847 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_031409.4	c.-97-4817C>T		intron_variant		ENST00000341935.10
CCR6	NM_001394582.1	c.-97-4817C>T		intron_variant
CCR6	NM_004367.6	c.-97-4817C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR6	ENST00000341935.10	c.-97-4817C>T		intron_variant		1	NM_031409.4	P1
	ENST00000647254.1	n.352G>A		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14981 AN: 152160 Hom.: 844 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0974

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0986 AC: 15012 AN: 152278 Hom.: 847 Cov.: 32 AF XY: 0.0983 AC XY: 7318 AN XY: 74454

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0833

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.109 Hom.: 1130

Bravo AF: 0.0973

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.67
Dann	Benign	0.60

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: rs3798315; hg19: chr6-167544709;