Variant rs3830355 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000257290.10(PDGFRA):c.2440-50_2440-49insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 1,600,954 control chromosomes in the GnomAD database, including 558,022 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 45100 hom., cov: 0)

Exomes 𝑓: 0.84 ( 512922 hom. )

Consequence

PDGFRA
ENST00000257290.10 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter U:1B:1

Conservation

PhyloP100: -1.30

Variant links:

Genes affected

PDGFRA (HGNC:8803): (platelet derived growth factor receptor alpha) This gene encodes 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 or a heterodimer, composed of both platelet-derived growth factor receptor alpha and beta polypeptides. Studies suggest that this gene plays a role in organ development, wound healing, and tumor progression. Mutations in this gene have been associated with idiopathic hypereosinophilic syndrome, somatic and familial gastrointestinal stromal tumors, and a variety of other cancers. [provided by RefSeq, Mar 2012]

PDGFRA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-54285791-T-TA is Benign according to our data. Variant chr4-54285791-T-TA is described in ClinVar as [Benign]. Clinvar id is 873180.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDGFRA	NM_006206.6 linkuse as main transcript	c.2440-50_2440-49insA		intron_variant		ENST00000257290.10	NP_006197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDGFRA	ENST00000257290.10 linkuse as main transcript	c.2440-50_2440-49insA		intron_variant		1	NM_006206.6	ENSP00000257290	P1	P16234-1

Frequencies

GnomAD3 genomes

AF:

0.757

AC:

114952

AN:

151914

Hom.:

45087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.535

Gnomad AMI

AF:

0.878

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.931

Gnomad EAS

AF:

0.851

Gnomad SAS

AF:

0.763

Gnomad FIN

AF:

0.870

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.856

Gnomad OTH

AF:

0.801

GnomAD3 exomes

AF:

0.805

AC:

201018

AN:

249854

Hom.:

82184

AF XY:

0.814

AC XY:

110044

AN XY:

135140

show subpopulations

Gnomad AFR exome

AF:

0.525

Gnomad AMR exome

AF:

0.677

Gnomad ASJ exome

AF:

0.925

Gnomad EAS exome

AF:

0.850

Gnomad SAS exome

AF:

0.782

Gnomad FIN exome

AF:

0.874

Gnomad NFE exome

AF:

0.857

Gnomad OTH exome

AF:

0.840

GnomAD4 exome

AF:

0.839

AC:

1215338

AN:

1448922

Hom.:

512922

Cov.:

AF XY:

0.840

AC XY:

606287

AN XY:

721696

show subpopulations

Gnomad4 AFR exome

AF:

0.524

Gnomad4 AMR exome

AF:

0.686

Gnomad4 ASJ exome

AF:

0.921

Gnomad4 EAS exome

AF:

0.853

Gnomad4 SAS exome

AF:

0.785

Gnomad4 FIN exome

AF:

0.875

Gnomad4 NFE exome

AF:

0.855

Gnomad4 OTH exome

AF:

0.835

GnomAD4 genome

AF:

0.756

AC:

115005

AN:

152032

Hom.:

45100

Cov.:

AF XY:

0.758

AC XY:

56361

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.534

Gnomad4 AMR

AF:

0.747

Gnomad4 ASJ

AF:

0.931

Gnomad4 EAS

AF:

0.851

Gnomad4 SAS

AF:

0.763

Gnomad4 FIN

AF:

0.870

Gnomad4 NFE

AF:

0.856

Gnomad4 OTH

AF:

0.802

Alfa

AF:

0.828

Hom.:

8179

Bravo

AF:

0.737

Asia WGS

AF:

0.763

AC:

2653

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Uncertain:1Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Squamous cell lung carcinoma

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing;in vivo

Faculté Pluridciplinaire Nador, Université Mohamed Premier

May 05, 2020

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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