Genetic Variant CCR3:n.331G>T (chr3-46264639-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000484025.5(CCR3):n.331G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 538,288 control chromosomes in the GnomAD database, including 24,675 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 0.27 ( 5969 hom., cov: 31)

Exomes 𝑓: 0.29 ( 18706 hom. )

Consequence

CCR3
ENST00000484025.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.451

Publications

9 publications found

Variant links:

Genes affected

CCR3 (HGNC:1604): (C-C motif chemokine receptor 3) The protein encoded by this gene is a receptor for C-C type chemokines. It belongs to family 1 of the G protein-coupled receptors. This receptor binds and responds to a variety of chemokines, including eotaxin (CCL11), eotaxin-3 (CCL26), MCP-3 (CCL7), MCP-4 (CCL13), and RANTES (CCL5). It is highly expressed in eosinophils and basophils, and is also detected in TH1 and TH2 cells, as well as in airway epithelial cells. This receptor may contribute to the accumulation and activation of eosinophils and other inflammatory cells in the allergic airway. It is also known to be an entry co-receptor for HIV-1. This gene and seven other chemokine receptor genes form a chemokine receptor gene cluster on the chromosomal region 3p21. Alternatively spliced transcript variants have been described. [provided by RefSeq, Sep 2009]

CCR3 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR3	NM_178329.3 link	c.-11-509G>T		intron_variant	Intron 1 of 1	ENST00000395940.3	NP_847899.1	P51677-1A1LPE5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR3	ENST00000395940.3 link	c.-11-509G>T		intron_variant	Intron 1 of 1	1	NM_178329.3	ENSP00000379271.2		P51677-1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

40862

AN:

151582

Hom.:

5948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.277

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.603

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.289

GnomAD4 exome

AF:

0.295

AC:

114020

AN:

386592

Hom.:

18706

Cov.:

AF XY:

0.301

AC XY:

61897

AN XY:

205716

show subpopulations

African (AFR)

AF:

0.222

AC:

1887

AN:

8512

American (AMR)

AF:

0.344

AC:

3841

AN:

11174

Ashkenazi Jewish (ASJ)

AF:

0.325

AC:

3942

AN:

12120

East Asian (EAS)

AF:

0.588

AC:

14083

AN:

23956

South Asian (SAS)

AF:

0.405

AC:

14936

AN:

36854

European-Finnish (FIN)

AF:

0.268

AC:

7317

AN:

27252

Middle Eastern (MID)

AF:

0.388

AC:

730

AN:

1880

European-Non Finnish (NFE)

AF:

0.251

AC:

60642

AN:

242064

Other (OTH)

AF:

0.292

AC:

6642

AN:

22780

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

3548

7095

10643

14190

17738

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

350

700

1050

1400

1750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.270

AC:

40916

AN:

151696

Hom.:

5969

Cov.:

AF XY:

0.276

AC XY:

20417

AN XY:

74102

show subpopulations

African (AFR)

AF:

0.220

AC:

9098

AN:

41336

American (AMR)

AF:

0.313

AC:

4777

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1117

AN:

3470

East Asian (EAS)

AF:

0.603

AC:

3116

AN:

5164

South Asian (SAS)

AF:

0.423

AC:

2028

AN:

4794

European-Finnish (FIN)

AF:

0.264

AC:

2764

AN:

10480

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.251

AC:

17035

AN:

67896

Other (OTH)

AF:

0.296

AC:

623

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1489

2978

4467

5956

7445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

432

864

1296

1728

2160

<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:

0.251

Hom.:

1490

Bravo

AF:

0.273

Asia WGS

AF:

0.482

AC:

1668

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.4

(source)

DANN

Benign

0.21

PhyloP100

0.45

PromoterAI

0.0041

Neutral

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over