rs17282391

Variant summary

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

The ENST00000684109.1(CCR3):​n.691+6409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,184 control chromosomes in the GnomAD database, including 624 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 0.071 ( 624 hom., cov: 32)

Consequence

CCR3
ENST00000684109.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19

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]

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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCR3ENST00000684109.1 linkn.691+6409A>G intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.0712
AC:
10832
AN:
152066
Hom.:
625
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0133
Gnomad AMI
AF:
0.182
Gnomad AMR
AF:
0.0513
Gnomad ASJ
AF:
0.110
Gnomad EAS
AF:
0.0454
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.0815
Gnomad OTH
AF:
0.0650
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0711
AC:
10820
AN:
152184
Hom.:
624
Cov.:
32
AF XY:
0.0786
AC XY:
5846
AN XY:
74414
show subpopulations
African (AFR)
AF:
0.0132
AC:
549
AN:
41516
American (AMR)
AF:
0.0512
AC:
782
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.110
AC:
383
AN:
3468
East Asian (EAS)
AF:
0.0453
AC:
235
AN:
5186
South Asian (SAS)
AF:
0.275
AC:
1322
AN:
4816
European-Finnish (FIN)
AF:
0.158
AC:
1670
AN:
10582
Middle Eastern (MID)
AF:
0.133
AC:
39
AN:
294
European-Non Finnish (NFE)
AF:
0.0814
AC:
5537
AN:
68008
Other (OTH)
AF:
0.0648
AC:
137
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
488
976
1465
1953
2441
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
150
300
450
600
750
<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:
0.0796
Hom.:
90
Bravo
AF:
0.0557
Asia WGS
AF:
0.139
AC:
483
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.7
DANN
Benign
0.54
PhyloP100
1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs17282391; hg19: chr3-46179481; API