rs3181077

Positions:

• chr3-46209161-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000357422.2(CCR3):​c.-284-1530C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,196 control chromosomes in the GnomAD database, including 49,605 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 0.80 (49605 hom., cov: 31)
• Consequence: CCR3 ENST00000357422.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR3	ENST00000357422.2	c.-284-1530C>T		intron_variant		2		ENSP00000350003	P1

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121914 AN: 152078 Hom.: 49553 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.807

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.802 AC: 122024 AN: 152196 Hom.: 49605 Cov.: 31 AF XY: 0.803 AC XY: 59755 AN XY: 74392

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.810

Alfa AF: 0.779 Hom.: 11167

Bravo AF: 0.814

Asia WGS AF: 0.872 AC: 3030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.42

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

LitVar

Other links and lift over

dbSNP: rs3181077; hg19: chr3-46250652;