rs3093010

Positions:

• chr6-167135119-C-A

Variant summary

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

The NM_031409.4(CCR6):​c.-97-919C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,176 control chromosomes in the GnomAD database, including 7,515 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 0.29 (7512 hom., cov: 32)
  • Exomes 𝑓: 0.30 (3 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR6	NM_031409.4	c.-97-919C>A		intron_variant		ENST00000341935.10	NP_113597.2
CCR6	NM_001394582.1	c.-97-919C>A		intron_variant			NP_001381511.1
CCR6	NM_004367.6	c.-97-919C>A		intron_variant			NP_004358.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10	c.-97-919C>A		intron_variant		1	NM_031409.4	ENSP00000343952.5
ENSG00000272980	ENST00000705249.1	c.1066-919C>A		intron_variant				ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44455 AN: 151972 Hom.: 7508 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.302 AC: 26 AN: 86 Hom.: 3 AF XY: 0.279 AC XY: 19 AN XY: 68

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.269

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.292 AC: 44472 AN: 152090 Hom.: 7512 Cov.: 32 AF XY: 0.299 AC XY: 22219 AN XY: 74340

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.284

Alfa AF: 0.324 Hom.: 11190

Bravo AF: 0.287

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3093010; hg19: chr6-167548607; COSMIC: COSV59476048; COSMIC: COSV59476048;