6-167112608-T-C

Variant names:

• chr6-167112608-T-C
• rs968334
• ENST00000705249.1:c.1066-23430T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000705249.1(ENSG00000272980):​c.1066-23430T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,876 control chromosomes in the GnomAD database, including 28,025 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 0.60 (28025 hom., cov: 31)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR6	NM_004367.6	c.-98+594T>C		intron_variant	Intron 1 of 2		NP_004358.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272980	ENST00000705249.1	c.1066-23430T>C		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91731 AN: 151758 Hom.: 27970 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.605 AC: 91837 AN: 151876 Hom.: 28025 Cov.: 31 AF XY: 0.603 AC XY: 44780 AN XY: 74232

African (AFR) AF: 0.684 AC: 28327 AN: 41408

American (AMR) AF: 0.628 AC: 9584 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2055 AN: 3462

East Asian (EAS) AF: 0.612 AC: 3157 AN: 5162

South Asian (SAS) AF: 0.618 AC: 2954 AN: 4782

European-Finnish (FIN) AF: 0.558 AC: 5882 AN: 10548

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37684 AN: 67938

Other (OTH) AF: 0.619 AC: 1305 AN: 2108

Alfa AF: 0.585 Hom.: 3244

Bravo AF: 0.615

Asia WGS AF: 0.652 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.57
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs968334; hg19: chr6-167526096; COSMIC: COSV68927967; COSMIC: COSV68927967;