ENST00000684109.1:n.691+13238C>A

Variant names:

• chr3-46144818-C-A
• rs7631551
• ENST00000684109.1:n.691+13238C>A

Variant summary

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

The ENST00000684109.1(CCR3):​n.691+13238C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,088 control chromosomes in the GnomAD database, including 2,094 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 0.14 (2094 hom., cov: 32)
• Consequence: CCR3 ENST00000684109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 13 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 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	ENST00000684109.1	n.691+13238C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21897 AN: 151970 Hom.: 2076 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.144 AC: 21948 AN: 152088 Hom.: 2094 Cov.: 32 AF XY: 0.149 AC XY: 11066 AN XY: 74322

African (AFR) AF: 0.259 AC: 10730 AN: 41436

American (AMR) AF: 0.0908 AC: 1389 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.0450 AC: 233 AN: 5178

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1677 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5684 AN: 67998

Other (OTH) AF: 0.129 AC: 272 AN: 2116

Alfa AF: 0.110 Hom.: 622

Bravo AF: 0.141

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.25
PhyloP100		0.086

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7631551; hg19: chr3-46186310;