3-46254286-A-G

Position:

• chr3-46254286-A-G

Variant summary

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

The NM_178329.3(CCR3):​c.-11-10862A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,970 control chromosomes in the GnomAD database, including 27,958 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 0.60 (27958 hom., cov: 31)
• Consequence: CCR3 NM_178329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

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]

CCR3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR3	NM_178329.3	c.-11-10862A>G		intron_variant		ENST00000395940.3	NP_847899.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR3	ENST00000395940.3	c.-11-10862A>G		intron_variant		1	NM_178329.3	ENSP00000379271.2

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91215 AN: 151852 Hom.: 27922 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.601 AC: 91296 AN: 151970 Hom.: 27958 Cov.: 31 AF XY: 0.609 AC XY: 45235 AN XY: 74268

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.634

Alfa AF: 0.571 Hom.: 41951

Bravo AF: 0.609

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.69

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: rs6441948; hg19: chr3-46295777;