rs13084057
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
ENST00000451650.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.13
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=-0.67).
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: 14750AN: 152150Hom.: 829 Cov.: 32
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GnomAD4 exome AF: 0.118 AC: 74983AN: 637122Hom.: 6100 Cov.: 6 AF XY: 0.127 AC XY: 43844AN XY: 346038
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GnomAD4 genome ? AF: 0.0969 AC: 14762AN: 152268Hom.: 831 Cov.: 32 AF XY: 0.104 AC XY: 7715AN XY: 74456
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at