chr3-46144818-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000684109.1(CCR3):​n.691+13238C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,088 control chromosomes in the GnomAD database, including 2,094 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 0.14 ( 2094 hom., cov: 32)

Consequence

CCR3
ENST00000684109.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCR3ENST00000684109.1 linkuse as main transcriptn.691+13238C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.144
AC:
21897
AN:
151970
Hom.:
2076
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.258
Gnomad AMI
AF:
0.182
Gnomad AMR
AF:
0.0911
Gnomad ASJ
AF:
0.120
Gnomad EAS
AF:
0.0451
Gnomad SAS
AF:
0.276
Gnomad FIN
AF:
0.159
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.0836
Gnomad OTH
AF:
0.129
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.144
AC:
21948
AN:
152088
Hom.:
2094
Cov.:
32
AF XY:
0.149
AC XY:
11066
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.259
Gnomad4 AMR
AF:
0.0908
Gnomad4 ASJ
AF:
0.120
Gnomad4 EAS
AF:
0.0450
Gnomad4 SAS
AF:
0.276
Gnomad4 FIN
AF:
0.159
Gnomad4 NFE
AF:
0.0836
Gnomad4 OTH
AF:
0.129
Alfa
AF:
0.112
Hom.:
582
Bravo
AF:
0.141
Asia WGS
AF:
0.165
AC:
575
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.75
DANN
Benign
0.25

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7631551; hg19: chr3-46186310; API