dbSNP rs3093026: ENSG00000272980:c.1066-16836C>T (chr6-167119202-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000705249.1(ENSG00000272980):c.1066-16836C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,190 control chromosomes in the GnomAD database, including 14,969 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 0.44 ( 14946 hom., cov: 32)

Exomes 𝑓: 0.46 ( 23 hom. )

Consequence

ENSG00000272980
ENST00000705249.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.919

Publications

11 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR6	NM_004367.6 link	c.-98+7188C>T		intron_variant	Intron 1 of 2		NP_004358.2	P51684

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272980	ENST00000705249.1 link	c.1066-16836C>T		intron_variant	Intron 11 of 12			ENSP00000516101.1		A0A994J5H4

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

66148

AN:

151862

Hom.:

14922

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.480

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.454

GnomAD4 exome

AF:

0.458

AC:

AN:

212

Hom.:

Cov.:

AF XY:

0.444

AC XY:

AN XY:

108

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.548

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.435

AC:

AN:

138

Other (OTH)

AF:

0.313

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.436

AC:

66221

AN:

151978

Hom.:

14946

Cov.:

AF XY:

0.435

AC XY:

32331

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.318

AC:

13188

AN:

41426

American (AMR)

AF:

0.535

AC:

8174

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.480

AC:

1668

AN:

3472

East Asian (EAS)

AF:

0.381

AC:

1968

AN:

5166

South Asian (SAS)

AF:

0.408

AC:

1965

AN:

4814

European-Finnish (FIN)

AF:

0.494

AC:

5213

AN:

10548

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.476

AC:

32350

AN:

67948

Other (OTH)

AF:

0.460

AC:

973

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1859

3719

5578

7438

9297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.423

Hom.:

6005

Bravo

AF:

0.439

Asia WGS

AF:

0.407

AC:

1413

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.8

(source)

DANN

Benign

0.33

PhyloP100

-0.92

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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rs3093026

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over