6-167138625-C-T

Position:

• chr6-167138625-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_031409.4(CCR6):​c.*1270C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 152,244 control chromosomes in the GnomAD database, including 21 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 0.016 (21 hom., cov: 31)
  • Exomes 𝑓: 0.029 (0 hom.)
• Consequence: CCR6 NM_031409.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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]

LOC112267970 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0162 (2465/152106) while in subpopulation AFR AF= 0.0188 (781/41472). AF 95% confidence interval is 0.0177. There are 21 homozygotes in gnomad4. There are 1180 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR6	NM_031409.4	c.*1270C>T		3_prime_UTR_variant	3/3	ENST00000341935.10	NP_113597.2
LOC112267970	XR_002956379.2	n.2236G>A		non_coding_transcript_exon_variant	2/2
CCR6	NM_001394582.1	c.*1270C>T		3_prime_UTR_variant	4/4		NP_001381511.1
CCR6	NM_004367.6	c.*1270C>T		3_prime_UTR_variant	3/3		NP_004358.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10	c.*1270C>T		3_prime_UTR_variant	3/3	1	NM_031409.4	ENSP00000343952	P1
CCR6	ENST00000349984.6	c.*1270C>T		3_prime_UTR_variant	4/4	1		ENSP00000339393	P1
CCR6	ENST00000400926.5	c.*1270C>T		3_prime_UTR_variant	3/3	2		ENSP00000383715	P1

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 2454 AN: 151988 Hom.: 20 Cov.: 31

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.00910

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0211

GnomAD4 exome AF: 0.0290 AC: 4 AN: 138 Hom.: 0 Cov.: 0 AF XY: 0.0135 AC XY: 1 AN XY: 74

Gnomad4 EAS exome AF: 0.0294

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0162 AC: 2465 AN: 152106 Hom.: 21 Cov.: 31 AF XY: 0.0159 AC XY: 1180 AN XY: 74368

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.00910

Gnomad4 NFE AF: 0.0177

Gnomad4 OTH AF: 0.0209

Alfa AF: 0.0182 Hom.: 11

Bravo AF: 0.0166

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.56

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: rs11575083; hg19: chr6-167552113;