rs62436827

Variant names:

• chr6-167135059-A-G
• rs62436827
• NM_031409.4:c.-97-979A>G

Variant summary

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

The NM_031409.4(CCR6):​c.-97-979A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0704 in 152,340 control chromosomes in the GnomAD database, including 509 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 0.070 (508 hom., cov: 33)
  • Exomes 𝑓: 0.076 (1 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031409.4. 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_031409.4	MANE Select	c.-97-979A>G		intron	N/A	NP_113597.2
	CCR6	NM_001394582.1		c.-97-979A>G		intron	N/A	NP_001381511.1	P51684
	CCR6	NM_004367.6		c.-97-979A>G		intron	N/A	NP_004358.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR6	ENST00000341935.10	TSL:1 MANE Select	c.-97-979A>G		intron	N/A	ENSP00000343952.5	P51684
	ENSG00000272980	ENST00000705249.1		c.1066-979A>G		intron	N/A	ENSP00000516101.1	A0A994J5H4
	CCR6	ENST00000349984.6	TSL:1	c.-97-979A>G		intron	N/A	ENSP00000339393.4	P51684

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10713 AN: 152104 Hom.: 509 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0545

GnomAD4 exome AF: 0.0763 AC: 9 AN: 118 Hom.: 1 Cov.: 0 AF XY: 0.0816 AC XY: 8 AN XY: 98

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

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

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0625 AC: 6 AN: 96

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.0704 AC: 10714 AN: 152222 Hom.: 508 Cov.: 33 AF XY: 0.0730 AC XY: 5431 AN XY: 74420

African (AFR) AF: 0.0159 AC: 660 AN: 41546

American (AMR) AF: 0.103 AC: 1568 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.0692 AC: 358 AN: 5176

South Asian (SAS) AF: 0.0750 AC: 361 AN: 4816

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10592

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0876 AC: 5958 AN: 68010

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0766 Hom.: 853

Bravo AF: 0.0639

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.85
DANN	Benign	0.29
PhyloP100		0.062
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: rs62436827; hg19: chr6-167548547;