rs13067058

Positions:

• chr3-46232275-G-A

Variant summary

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

The ENST00000357422.2(CCR3):​c.-67-10127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 152,252 control chromosomes in the GnomAD database, including 418 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 0.059 (418 hom., cov: 32)
• Consequence: CCR3 ENST00000357422.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR3	XM_006712960.4	c.-67-10127G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR3	ENST00000357422.2	c.-67-10127G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8939 AN: 152134 Hom.: 418 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0587 AC: 8931 AN: 152252 Hom.: 418 Cov.: 32 AF XY: 0.0641 AC XY: 4769 AN XY: 74436

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.0382

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0627 Hom.: 69

Bravo AF: 0.0473

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.47

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: rs13067058; hg19: chr3-46273766;