rs3828610

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.445
Variant links:
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
PDGFRBNM_002609.4 linkc.-672T>G upstream_gene_variant ENST00000261799.9 NP_002600.1 P09619-1Q59F04
PDGFRBNM_001355016.2 linkc.-818T>G upstream_gene_variant NP_001341945.1
PDGFRBNM_001355017.2 linkc.-1189T>G upstream_gene_variant NP_001341946.1
PDGFRBNR_149150.2 linkn.-217T>G upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PDGFRBENST00000261799.9 linkc.-672T>G upstream_gene_variant 1 NM_002609.4 ENSP00000261799.4 P09619-1
PDGFRBENST00000520579.5 linkn.-672T>G upstream_gene_variant 1 ENSP00000430026.1 E5RH16
PDGFRBENST00000517660.1 linkn.-202T>G upstream_gene_variant 3
PDGFRBENST00000523456.1 linkn.-190T>G upstream_gene_variant 2

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
73479
AN:
150848
Hom.:
19619
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.719
Gnomad AMI
AF:
0.319
Gnomad AMR
AF:
0.450
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.580
Gnomad SAS
AF:
0.402
Gnomad FIN
AF:
0.337
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.374
Gnomad OTH
AF:
0.495
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.487
AC:
73587
AN:
150962
Hom.:
19661
Cov.:
31
AF XY:
0.484
AC XY:
35696
AN XY:
73684
show subpopulations
Gnomad4 AFR
AF:
0.720
Gnomad4 AMR
AF:
0.450
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.579
Gnomad4 SAS
AF:
0.402
Gnomad4 FIN
AF:
0.337
Gnomad4 NFE
AF:
0.374
Gnomad4 OTH
AF:
0.495
Alfa
AF:
0.453
Hom.:
1587
Bravo
AF:
0.506
Asia WGS
AF:
0.491
AC:
1707
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
19
DANN
Benign
0.85

Splicing

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: rs3828610; hg19: chr5-149535625; API