rs13084057

Positions:

• chr3-46143233-C-G
• chr3-46143233-C-T

Variant summary

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

The ENST00000451650.1(FLT1P1):​n.445G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.114 in 789,390 control chromosomes in the GnomAD database, including 6,931 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 0.097 (831 hom., cov: 32)
  • Exomes 𝑓: 0.12 (6100 hom.)
• Consequence: FLT1P1 ENST00000451650.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.13

Genes affected

FLT1P1 (HGNC:44609): (FLT1 pseudogene 1)

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLT1P1	ENST00000451650.1	n.445G>C		non_coding_transcript_exon_variant	1/1
CCR3	ENST00000684109.1	n.691+11653C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14750 AN: 152150 Hom.: 829 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0855

GnomAD4 exome AF: 0.118 AC: 74983 AN: 637122 Hom.: 6100 Cov.: 6 AF XY: 0.127 AC XY: 43844 AN XY: 346038

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.0556

Gnomad4 ASJ exome AF: 0.113

Gnomad4 EAS exome AF: 0.0477

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.0964

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.0969 AC: 14762 AN: 152268 Hom.: 831 Cov.: 32 AF XY: 0.104 AC XY: 7715 AN XY: 74456

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0627

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0447

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.0851

Alfa AF: 0.0437 Hom.: 36

Bravo AF: 0.0860

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	10
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13084057; hg19: chr3-46184725;