GeneBe

NM_002609.4:c.2844G>C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_002609.4(PDGFRB):​c.2844G>C​(p.Arg948Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R948R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PDGFRB
NM_002609.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890

Publications

5 publications found
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]
PDGFRB Gene-Disease associations (from GenCC):
  • acroosteolysis-keloid-like lesions-premature aging syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
  • myofibromatosis, infantile, 1
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
  • skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
  • basal ganglia calcification, idiopathic, 4
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
  • bilateral striopallidodentate calcinosis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • infantile myofibromatosis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • hereditary progressive mucinous histiocytosis
    Inheritance: AD Classification: LIMITED Submitted by: G2P

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BP7
Synonymous conserved (PhyloP=-0.089 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PDGFRBNM_002609.4 linkc.2844G>C p.Arg948Arg synonymous_variant Exon 21 of 23 ENST00000261799.9 NP_002600.1 P09619-1Q59F04
PDGFRBNM_001355016.2 linkc.2652G>C p.Arg884Arg synonymous_variant Exon 20 of 22 NP_001341945.1
PDGFRBNM_001355017.2 linkc.2361G>C p.Arg787Arg synonymous_variant Exon 21 of 23 NP_001341946.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PDGFRBENST00000261799.9 linkc.2844G>C p.Arg948Arg synonymous_variant Exon 21 of 23 1 NM_002609.4 ENSP00000261799.4 P09619-1
PDGFRBENST00000520579.5 linkn.*2158G>C non_coding_transcript_exon_variant Exon 21 of 23 1 ENSP00000430026.1 E5RH16
PDGFRBENST00000520579.5 linkn.*2158G>C 3_prime_UTR_variant Exon 21 of 23 1 ENSP00000430026.1 E5RH16

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1461158
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
726902
African (AFR)
AF:
0.00
AC:
0
AN:
33460
American (AMR)
AF:
0.00
AC:
0
AN:
44688
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26118
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39690
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86212
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111450
Other (OTH)
AF:
0.00
AC:
0
AN:
60356
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
CADD
Benign
7.4
DANN
Benign
0.66
PhyloP100
-0.089
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs55647240; hg19: chr5-149498370; COSMIC: COSV55805140; COSMIC: COSV55805140; API