3-46193709-C-T

Variant names:

• chr3-46193709-C-T
• rs13098911
• ENST00000357422.2:c.-284-16982C>T

Variant summary

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

The ENST00000357422.2(CCR3):​c.-284-16982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,132 control chromosomes in the GnomAD database, including 615 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 (615 hom., cov: 32)
• Consequence: CCR3 ENST00000357422.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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
CCR3	ENST00000357422.2	c.-284-16982C>T		intron_variant	Intron 1 of 3	2		ENSP00000350003.2

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 10753 AN: 152014 Hom.: 616 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0706 AC: 10741 AN: 152132 Hom.: 615 Cov.: 32 AF XY: 0.0780 AC XY: 5800 AN XY: 74344

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.0808

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0809 Hom.: 941

Bravo AF: 0.0554

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	-0.80
CADD	Benign	12
DANN	Benign	0.79

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: rs13098911; hg19: chr3-46235201;