rs62436827

Positions:

• chr6-167135059-A-G

Variant summary

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

The NM_031409.4(CCR6):​c.-97-979A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0704 in 152,340 control chromosomes in the GnomAD database, including 509 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 0.070 (508 hom., cov: 33)
  • Exomes 𝑓: 0.076 (1 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_031409.4	c.-97-979A>G		intron_variant		ENST00000341935.10
CCR6	NM_001394582.1	c.-97-979A>G		intron_variant
CCR6	NM_004367.6	c.-97-979A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR6	ENST00000341935.10	c.-97-979A>G		intron_variant		1	NM_031409.4	P1
CCR6	ENST00000349984.6	c.-97-979A>G		intron_variant		1		P1
CCR6	ENST00000400926.5	c.-97-979A>G		intron_variant		2		P1
CCR6	ENST00000643861.1	c.-97-979A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10713 AN: 152104 Hom.: 509 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0545

GnomAD4 exome AF: 0.0763 AC: 9 AN: 118 Hom.: 1 Cov.: 0 AF XY: 0.0816 AC XY: 8 AN XY: 98

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.0625

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.0704 AC: 10714 AN: 152222 Hom.: 508 Cov.: 33 AF XY: 0.0730 AC XY: 5431 AN XY: 74420

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0692

Gnomad4 SAS AF: 0.0750

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0765 Hom.: 123

Bravo AF: 0.0639

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.85
DANN	Benign	0.29

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: rs62436827; hg19: chr6-167548547;