3-46164194-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_940805.3(LOC105377067):​n.389+332C>T variant causes a intron, non coding transcript 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

LOC105377067
XR_940805.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105377067XR_940805.3 linkuse as main transcriptn.389+332C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCR3ENST00000357422.2 linkuse as main transcriptc.-285+332C>T intron_variant 2 ENSP00000350003 P1P51677-1
CCR3ENST00000682778.1 linkuse as main transcriptn.647+332C>T intron_variant, non_coding_transcript_variant
CCR3ENST00000684109.1 linkuse as main transcriptn.692-24738C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.621
AC:
94227
AN:
151746
Hom.:
29686
Cov.:
30
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.536
Gnomad4 AMR
AF:
0.716
Gnomad4 ASJ
AF:
0.628
Gnomad4 EAS
AF:
0.879
Gnomad4 SAS
AF:
0.573
Gnomad4 FIN
AF:
0.604
Gnomad4 NFE
AF:
0.638
Gnomad4 OTH
AF:
0.657
Alfa
AF:
0.643
Hom.:
54573
Bravo
AF:
0.629
Asia WGS
AF:
0.706
AC:
2455
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
1.0
DANN
Benign
0.48

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7616215; hg19: chr3-46205686; API