rs3828610
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002609.4(PDGFRB):c.-672T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 150,962 control chromosomes in the GnomAD database, including 19,661 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 0.49 ( 19661 hom., cov: 31)
Consequence
PDGFRB
NM_002609.4 upstream_gene
NM_002609.4 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.445
Genes affected
PDGFRB (HGNC:8804): (platelet derived growth factor receptor beta) The protein encoded by this gene is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer (PDGFB or PDGFD) or a heterodimer (PDGFA and PDGFB). This gene is essential for normal development of the cardiovascular system and aids in rearrangement of the actin cytoskeleton. This gene is flanked on chromosome 5 by the genes for granulocyte-macrophage colony-stimulating factor and macrophage-colony stimulating factor receptor; all three genes may be implicated in the 5-q syndrome. A translocation between chromosomes 5 and 12, that fuses this gene to that of the ETV6 gene, results in chronic myeloproliferative disorder with eosinophilia. [provided by RefSeq, Aug 2017]
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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=-0.47).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDGFRB | NM_002609.4 | c.-672T>G | upstream_gene_variant | ENST00000261799.9 | NP_002600.1 | |||
PDGFRB | NM_001355016.2 | c.-818T>G | upstream_gene_variant | NP_001341945.1 | ||||
PDGFRB | NM_001355017.2 | c.-1189T>G | upstream_gene_variant | NP_001341946.1 | ||||
PDGFRB | NR_149150.2 | n.-217T>G | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFRB | ENST00000261799.9 | c.-672T>G | upstream_gene_variant | 1 | NM_002609.4 | ENSP00000261799.4 | ||||
PDGFRB | ENST00000520579.5 | n.-672T>G | upstream_gene_variant | 1 | ENSP00000430026.1 | |||||
PDGFRB | ENST00000517660.1 | n.-202T>G | upstream_gene_variant | 3 | ||||||
PDGFRB | ENST00000523456.1 | n.-190T>G | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.487 AC: 73479AN: 150848Hom.: 19619 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.487 AC: 73587AN: 150962Hom.: 19661 Cov.: 31 AF XY: 0.484 AC XY: 35696AN XY: 73684
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at