Genetic Variant CCR6:c.-97-979A>G (chr6-167135059-A-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_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0620

Publications

7 publications found

Variant links:

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]

CCR6 links:

ENSG00000272980 (HGNC:):

ENSG00000272980 links:

Genome browser will be placed here

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=-0.78).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCR6	NM_031409.4 link	c.-97-979A>G	intron_variant	Intron 1 of 2	ENST00000341935.10	NP_113597.2	P51684
CCR6	NM_001394582.1 link	c.-97-979A>G	intron_variant	Intron 2 of 3		NP_001381511.1
CCR6	NM_004367.6 link	c.-97-979A>G	intron_variant	Intron 1 of 2		NP_004358.2	P51684

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR6	ENST00000341935.10 link	c.-97-979A>G		intron_variant	Intron 1 of 2	1	NM_031409.4	ENSP00000343952.5		P51684
ENSG00000272980	ENST00000705249.1 link	c.1066-979A>G		intron_variant	Intron 11 of 12			ENSP00000516101.1		A0A994J5H4

Frequencies

GnomAD3 genomes

AF:

0.0704

AC:

10713

AN:

152104

Hom.:

509

Cov.:

show subpopulations

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:

AN:

118

Hom.:

Cov.:

AF XY:

0.0816

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0625

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.404

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0704

AC:

10714

AN:

152222

Hom.:

508

Cov.:

AF XY:

0.0730

AC XY:

5431

AN XY:

74420

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0876

AC:

5958

AN:

68010

Other (OTH)

AF:

0.0539

AC:

114

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

512

1024

1535

2047

2559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0766

Hom.:

853

Bravo

AF:

0.0639

Asia WGS

AF:

0.0570

AC:

200

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.85

(source)

DANN

Benign

0.29

PhyloP100

0.062

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over