Variant 5-150115724-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002609.4(PDGFRB):c.*39C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,522,516 control chromosomes in the GnomAD database, including 14,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1116 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12997 hom. )

Consequence

PDGFRB
NM_002609.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.523

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 5-150115724-G-C is Benign according to our data. Variant chr5-150115724-G-C is described in ClinVar as [Benign]. Clinvar id is 1182989.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
PDGFRB	NM_002609.4 linkuse as main transcript	c.*39C>G	3_prime_UTR_variant	23/23	ENST00000261799.9
PDGFRB	NM_001355016.2 linkuse as main transcript	c.*39C>G	3_prime_UTR_variant	22/22
PDGFRB	NM_001355017.2 linkuse as main transcript	c.*39C>G	3_prime_UTR_variant	23/23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFRB	ENST00000261799.9 linkuse as main transcript	c.*39C>G		3_prime_UTR_variant	23/23	1	NM_002609.4	P1	P09619-1
PDGFRB	ENST00000520579.5 linkuse as main transcript			downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17638

AN:

151394

Hom.:

1117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0955

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.0944

Gnomad FIN

AF:

0.0626

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.128

GnomAD3 exomes

AF:

0.101

AC:

17633

AN:

174612

Hom.:

1057

AF XY:

0.105

AC XY:

9911

AN XY:

94212

show subpopulations

Gnomad AFR exome

AF:

0.0887

Gnomad AMR exome

AF:

0.0746

Gnomad ASJ exome

AF:

0.175

Gnomad EAS exome

AF:

0.000849

Gnomad SAS exome

AF:

0.0796

Gnomad FIN exome

AF:

0.0668

Gnomad NFE exome

AF:

0.134

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

AF:

0.132

AC:

181267

AN:

1371002

Hom.:

12997

Cov.:

AF XY:

0.132

AC XY:

88806

AN XY:

673682

show subpopulations

Gnomad4 AFR exome

AF:

0.0899

Gnomad4 AMR exome

AF:

0.0800

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.000786

Gnomad4 SAS exome

AF:

0.0897

Gnomad4 FIN exome

AF:

0.0767

Gnomad4 NFE exome

AF:

0.144

Gnomad4 OTH exome

AF:

0.133

GnomAD4 genome

AF:

0.116

AC:

17636

AN:

151514

Hom.:

1116

Cov.:

AF XY:

0.111

AC XY:

8221

AN XY:

74098

show subpopulations

Gnomad4 AFR

AF:

0.0954

Gnomad4 AMR

AF:

0.115

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.0949

Gnomad4 FIN

AF:

0.0626

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.126

Alfa

AF:

0.0838

Hom.:

175

Bravo

AF:

0.122

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

8.5

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over