rs3093024

chr6-167119305-A-Gchr6-167119305-A-T

Variant summary

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

The ENST00000642778.1(ENSG00000284825):n.80T>C variant causes a non coding transcript exon 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: ENST00000642778.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

(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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR6	NM_004367.6	c.-98+7291A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642778.1	n.80T>C		non_coding_transcript_exon_variant	2/4
CCR6	ENST00000400926.5	c.-98+7291A>G		intron_variant		2		P1

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

Gnomad4 AFR exome AF: 0.611

Gnomad4 AMR exome AF: 0.625

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.595

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.526

Gnomad4 NFE exome AF: 0.506

Gnomad4 OTH exome AF: 0.450

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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.623

Alfa AF: 0.571 Hom.: 55174

Bravo AF: 0.620

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.80
Dann	Benign	0.11

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: rs3093024; hg19: chr6-167532793;