rs3093024

Variant names:

• chr6-167119305-A-G
• rs3093024
• ENST00000705249.1:c.1066-16733A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-167119305-A-G
• chr6-167119305-A-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+7291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,748 control chromosomes in the GnomAD database, including 28,463 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 (28368 hom., cov: 32)
  • Exomes 𝑓: 0.52 (95 hom.)
• Consequence: CCR6 NM_004367.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 77 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004367.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR6	NM_004367.6		c.-98+7291A>G		intron	N/A	NP_004358.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272980	ENST00000705249.1		c.1066-16733A>G		intron	N/A	ENSP00000516101.1	A0A994J5H4
	CCR6	ENST00000400926.5	TSL:2	c.-98+7291A>G		intron	N/A	ENSP00000383715.2	P51684
	CCR6	ENST00000884634.1		c.-335-3814A>G		intron	N/A	ENSP00000554693.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92310 AN: 151886 Hom.: 28309 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.617

GnomAD4 exome AF: 0.517 AC: 385 AN: 744 Hom.: 95 Cov.: 0 AF XY: 0.522 AC XY: 194 AN XY: 372

African (AFR) AF: 0.611 AC: 11 AN: 18

American (AMR) AF: 0.625 AC: 10 AN: 16

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 9 AN: 18

East Asian (EAS) AF: 0.595 AC: 44 AN: 74

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.526 AC: 40 AN: 76

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.506 AC: 251 AN: 496

Other (OTH) AF: 0.450 AC: 18 AN: 40

GnomAD4 genome AF: 0.608 AC: 92428 AN: 152004 Hom.: 28368 Cov.: 32 AF XY: 0.605 AC XY: 44964 AN XY: 74292

African (AFR) AF: 0.686 AC: 28406 AN: 41436

American (AMR) AF: 0.649 AC: 9924 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3468

East Asian (EAS) AF: 0.571 AC: 2946 AN: 5158

South Asian (SAS) AF: 0.607 AC: 2916 AN: 4804

European-Finnish (FIN) AF: 0.546 AC: 5767 AN: 10558

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38262 AN: 67972

Other (OTH) AF: 0.623 AC: 1316 AN: 2114

Alfa AF: 0.576 Hom.: 108480

Bravo AF: 0.620

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.11
PhyloP100		-2.0
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: rs3093024; hg19: chr6-167532793;