dbSNP rs6927645: ENSG00000272980:c.1066-19224C>G (chr6-167116814-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004367.6(CCR6):c.-98+4800C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,348 control chromosomes in the GnomAD database, including 2,921 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 0.16 ( 2920 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1 hom. )

Consequence

CCR6
NM_004367.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.10

Publications

8 publications found

Variant links:

Genes affected

ENSG00000272980 (HGNC:):

ENSG00000272980 links:

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]

CCR6 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004367.6. 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_004367.6		c.-98+4800C>G		intron	N/A	NP_004358.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000272980	ENST00000705249.1		c.1066-19224C>G	intron	N/A	ENSP00000516101.1	A0A994J5H4
CCR6	ENST00000400926.5	TSL:2	c.-98+4800C>G	intron	N/A	ENSP00000383715.2	P51684
CCR6	ENST00000884634.1		c.-336+4800C>G	intron	N/A	ENSP00000554693.1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24537

AN:

152138

Hom.:

2903

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.0633

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0855

Gnomad OTH

AF:

0.155

GnomAD4 exome

AF:

0.0435

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0417

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0233

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.162

AC:

24597

AN:

152256

Hom.:

2920

Cov.:

AF XY:

0.159

AC XY:

11877

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.328

AC:

13626

AN:

41520

American (AMR)

AF:

0.111

AC:

1692

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

417

AN:

3468

East Asian (EAS)

AF:

0.194

AC:

1004

AN:

5180

South Asian (SAS)

AF:

0.197

AC:

951

AN:

4832

European-Finnish (FIN)

AF:

0.0633

AC:

672

AN:

10620

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0855

AC:

5817

AN:

68014

Other (OTH)

AF:

0.158

AC:

333

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

957

1915

2872

3830

4787

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.126

Hom.:

227

Bravo

AF:

0.169

Asia WGS

AF:

0.227

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.80

(source)

DANN

Benign

0.19

PhyloP100

-3.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over