3-46164194-C-T

Variant names:

• chr3-46164194-C-T
• rs7616215
• ENST00000357422.2:c.-285+332C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000357422.2(CCR3):​c.-285+332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,864 control chromosomes in the GnomAD database, including 29,714 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 0.62 (29714 hom., cov: 30)
• Consequence: CCR3 ENST00000357422.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 65 publications found

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]

LOC105377067 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000357422.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR3	ENST00000357422.2	TSL:2	c.-285+332C>T		intron	N/A	ENSP00000350003.2	P51677-1
	CCR3	ENST00000682778.1		n.647+332C>T		intron	N/A
	CCR3	ENST00000684109.1		n.692-24738C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94227 AN: 151746 Hom.: 29686 Cov.: 30

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.621 AC: 94281 AN: 151864 Hom.: 29714 Cov.: 30 AF XY: 0.620 AC XY: 46031 AN XY: 74232

African (AFR) AF: 0.536 AC: 22171 AN: 41398

American (AMR) AF: 0.716 AC: 10936 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3470

East Asian (EAS) AF: 0.879 AC: 4542 AN: 5166

South Asian (SAS) AF: 0.573 AC: 2759 AN: 4812

European-Finnish (FIN) AF: 0.604 AC: 6364 AN: 10544

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43321 AN: 67898

Other (OTH) AF: 0.657 AC: 1383 AN: 2104

Alfa AF: 0.639 Hom.: 126067

Bravo AF: 0.629

Asia WGS AF: 0.706 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7616215; hg19: chr3-46205686;