NM_031409.4:c.-97-4817C>T

Variant names:

• chr6-167131221-C-T
• rs3798315
• NM_031409.4:c.-97-4817C>T

Variant summary

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

The NM_031409.4(CCR6):​c.-97-4817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 152,294 control chromosomes in the GnomAD database, including 847 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 0.099 (847 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: CCR6 NM_031409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 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.-97-4817C>T		intron	N/A	NP_113597.2
	CCR6	NM_001394582.1		c.-97-4817C>T		intron	N/A	NP_001381511.1	P51684
	CCR6	NM_004367.6		c.-97-4817C>T		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.-97-4817C>T		intron	N/A	ENSP00000343952.5	P51684
	ENSG00000272980	ENST00000705249.1		c.1066-4817C>T		intron	N/A	ENSP00000516101.1	A0A994J5H4
	CCR6	ENST00000349984.6	TSL:1	c.-97-4817C>T		intron	N/A	ENSP00000339393.4	P51684

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14981 AN: 152160 Hom.: 844 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0974

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0986 AC: 15012 AN: 152278 Hom.: 847 Cov.: 32 AF XY: 0.0983 AC XY: 7318 AN XY: 74454

African (AFR) AF: 0.0553 AC: 2297 AN: 41568

American (AMR) AF: 0.109 AC: 1666 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.153 AC: 794 AN: 5180

South Asian (SAS) AF: 0.117 AC: 566 AN: 4818

European-Finnish (FIN) AF: 0.0833 AC: 884 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8205 AN: 68016

Other (OTH) AF: 0.0988 AC: 209 AN: 2116

Alfa AF: 0.109 Hom.: 1600

Bravo AF: 0.0973

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.67
DANN	Benign	0.60
PhyloP100		-2.7
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: rs3798315; hg19: chr6-167544709;