chr6-167127354-C-T

Position:

• chr6-167127354-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.-98+4131C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,942 control chromosomes in the GnomAD database, including 28,239 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 0.61 (28239 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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]

ENSG00000272980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR6	NM_031409.4	c.-98+4131C>T		intron_variant		ENST00000341935.10	NP_113597.2
CCR6	NM_001394582.1	c.-98+4131C>T		intron_variant			NP_001381511.1
CCR6	NM_004367.6	c.-97-8684C>T		intron_variant			NP_004358.2
LOC107986672	XR_001744470.2	n.-27G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10	c.-98+4131C>T		intron_variant		1	NM_031409.4	ENSP00000343952.5
ENSG00000272980	ENST00000705249.1	c.1066-8684C>T		intron_variant				ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92060 AN: 151818 Hom.: 28180 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.617

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.607 AC: 92178 AN: 151936 Hom.: 28239 Cov.: 31 AF XY: 0.603 AC XY: 44806 AN XY: 74252

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.623

Alfa AF: 0.604 Hom.: 4119

Bravo AF: 0.619

Asia WGS AF: 0.606 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.23

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: rs1571878; hg19: chr6-167540842; COSMIC: COSV59476043;