rs17708515

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001355016.2(PDGFRB):c.-91C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00742 in 1,579,558 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 49 hom., cov: 33)

Exomes 𝑓: 0.0070 ( 352 hom. )

Consequence

PDGFRB
NM_001355016.2 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.989

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 5-150135817-G-A is Benign according to our data. Variant chr5-150135817-G-A is described in ClinVar as [Benign]. Clinvar id is 473399.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-150135817-G-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFRB	NM_002609.4 link	c.102C>T	p.Val34Val	synonymous_variant	Exon 3 of 23	ENST00000261799.9	NP_002600.1	P09619-1Q59F04

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFRB	ENST00000261799.9 link	c.102C>T	p.Val34Val	synonymous_variant	Exon 3 of 23	1	NM_002609.4	ENSP00000261799.4		P09619-1

Frequencies

GnomAD3 genomes

AF:

0.0109

AC:

1656

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00956

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0366

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0360

Gnomad SAS

AF:

0.0599

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000838

Gnomad OTH

AF:

0.00767

GnomAD3 exomes

AF:

0.0212

AC:

4649

AN:

219058

Hom.:

187

AF XY:

0.0198

AC XY:

2323

AN XY:

117370

show subpopulations

Gnomad AFR exome

AF:

0.00875

Gnomad AMR exome

AF:

0.0776

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0306

Gnomad SAS exome

AF:

0.0522

Gnomad FIN exome

AF:

0.0152

Gnomad NFE exome

AF:

0.000901

Gnomad OTH exome

AF:

0.0142

GnomAD4 exome

AF:

0.00703

AC:

10030

AN:

1427270

Hom.:

352

Cov.:

AF XY:

0.00793

AC XY:

5606

AN XY:

706806

show subpopulations

Gnomad4 AFR exome

AF:

0.00938

Gnomad4 AMR exome

AF:

0.0723

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0245

Gnomad4 SAS exome

AF:

0.0497

Gnomad4 FIN exome

AF:

0.0154

Gnomad4 NFE exome

AF:

0.000381

Gnomad4 OTH exome

AF:

0.0113

GnomAD4 genome

AF:

0.0111

AC:

1683

AN:

152288

Hom.:

Cov.:

AF XY:

0.0125

AC XY:

934

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00991

Gnomad4 AMR

AF:

0.0371

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0361

Gnomad4 SAS

AF:

0.0593

Gnomad4 FIN

AF:

0.0141

Gnomad4 NFE

AF:

0.000838

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00371

Hom.:

Bravo

AF:

0.0125

Asia WGS

AF:

0.0630

AC:

219

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

PDGFRB-related disorder

Benign:1

Jun 08, 2022

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Myofibromatosis, infantile, 1

Benign:1

Feb 01, 2025

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Oct 08, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Myeloproliferative disorder, chronic, with eosinophilia

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Infantile myofibromatosis;C1866182:Acroosteolysis-keloid-like lesions-premature aging syndrome;C3554321:Basal ganglia calcification, idiopathic, 4;C4225270:Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome

Benign:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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