rs3093023

Variant names:

• chr6-167120802-G-A
• rs3093023
• ENST00000705249.1:c.1066-15236G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-167120802-G-A
• chr6-167120802-G-C
• chr6-167120802-G-T

Variant summary

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

The NM_004367.6(CCR6):​c.-98+8788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,140 control chromosomes in the GnomAD database, including 10,052 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 0.34 (10052 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: CCR6 NM_004367.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR6	NM_004367.6	c.-98+8788G>A		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.1066-15236G>A		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51905 AN: 152022 Hom.: 10055 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.341 AC: 51884 AN: 152140 Hom.: 10052 Cov.: 33 AF XY: 0.345 AC XY: 25661 AN XY: 74382

African (AFR) AF: 0.151 AC: 6281 AN: 41506

American (AMR) AF: 0.326 AC: 4984 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2225 AN: 5192

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4826

European-Finnish (FIN) AF: 0.452 AC: 4774 AN: 10558

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29449 AN: 67982

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.406 Hom.: 45554

Bravo AF: 0.322

Asia WGS AF: 0.352 AC: 1226 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	1.6
DANN	Benign	0.42
PhyloP100		0.028
PromoterAI		-0.0095	Neutral
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

Publications

LitVar

Other links and lift over

dbSNP: rs3093023; hg19: chr6-167534290;