rs17217831

chr3-46263950-C-A

Variant summary

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

The NM_178329.3(CCR3):c.-11-1198C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 155,710 control chromosomes in the GnomAD database, including 468 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 0.068 (456 hom., cov: 32)
  • Exomes 𝑓: 0.074 (12 hom.)
• Consequence: CCR3 NM_178329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR3	NM_178329.3	c.-11-1198C>A		intron_variant		ENST00000395940.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR3	ENST00000395940.3	c.-11-1198C>A		intron_variant		1	NM_178329.3	P1

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10424 AN: 152158 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0664

GnomAD4 exome AF: 0.0740 AC: 254 AN: 3434 Hom.: 12 Cov.: 0 AF XY: 0.0815 AC XY: 142 AN XY: 1742

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0492

Gnomad4 ASJ exome AF: 0.0952

Gnomad4 EAS exome AF: 0.0208

Gnomad4 SAS exome AF: 0.165

Gnomad4 FIN exome AF: 0.129

Gnomad4 NFE exome AF: 0.0648

Gnomad4 OTH exome AF: 0.0450

GnomAD4 genome AF: 0.0685 AC: 10425 AN: 152276 Hom.: 456 Cov.: 32 AF XY: 0.0736 AC XY: 5481 AN XY: 74440

Gnomad4 AFR AF: 0.0474

Gnomad4 AMR AF: 0.0445

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0363

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0685 Hom.: 106

Bravo AF: 0.0577

Asia WGS AF: 0.0920 AC: 318 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	1.4
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: rs17217831; hg19: chr3-46305441;