chr3-46235387-T-A

Variant names:

• chr3-46235387-T-A
• rs1388604
• ENST00000357422.2:c.-67-7015T>A

Variant summary

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

The ENST00000357422.2(CCR3):​c.-67-7015T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,042 control chromosomes in the GnomAD database, including 9,834 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 0.36 (9834 hom., cov: 32)
• Consequence: CCR3 ENST00000357422.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 10 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]

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 (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR3	XM_006712960.4	c.-67-7015T>A		intron_variant	Intron 1 of 2		XP_006713023.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR3	ENST00000357422.2	c.-67-7015T>A		intron_variant	Intron 2 of 3	2		ENSP00000350003.2

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53925 AN: 151924 Hom.: 9807 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.355 AC: 53998 AN: 152042 Hom.: 9834 Cov.: 32 AF XY: 0.349 AC XY: 25943 AN XY: 74324

African (AFR) AF: 0.418 AC: 17333 AN: 41474

American (AMR) AF: 0.375 AC: 5735 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1367 AN: 5168

South Asian (SAS) AF: 0.176 AC: 848 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2727 AN: 10592

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23670 AN: 67932

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.346 Hom.: 1174

Bravo AF: 0.367

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.46
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: rs1388604; hg19: chr3-46276878;