Variant 4-54295087-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006206.6(PDGFRA):c.3123-38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 1,598,460 control chromosomes in the GnomAD database, including 560,243 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.75 ( 44288 hom., cov: 32)

Exomes 𝑓: 0.84 ( 515955 hom. )

Consequence

PDGFRA
NM_006206.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.817

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 4-54295087-C-T is Benign according to our data. Variant chr4-54295087-C-T is described in ClinVar as [Benign]. Clinvar id is 259952.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFRA	NM_006206.6 linkuse as main transcript	c.3123-38C>T		intron_variant		ENST00000257290.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFRA	ENST00000257290.10 linkuse as main transcript	c.3123-38C>T		intron_variant		1	NM_006206.6	P1	P16234-1

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113258

AN:

151928

Hom.:

44277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.878

Gnomad AMR

AF:

0.738

Gnomad ASJ

AF:

0.927

Gnomad EAS

AF:

0.857

Gnomad SAS

AF:

0.761

Gnomad FIN

AF:

0.870

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.861

Gnomad OTH

AF:

0.790

GnomAD3 exomes

AF:

0.804

AC:

201190

AN:

250382

Hom.:

82432

AF XY:

0.814

AC XY:

110188

AN XY:

135350

show subpopulations

Gnomad AFR exome

AF:

0.477

Gnomad AMR exome

AF:

0.673

Gnomad ASJ exome

AF:

0.921

Gnomad EAS exome

AF:

0.859

Gnomad SAS exome

AF:

0.782

Gnomad FIN exome

AF:

0.874

Gnomad NFE exome

AF:

0.861

Gnomad OTH exome

AF:

0.840

GnomAD4 exome

AF:

0.841

AC:

1217052

AN:

1446414

Hom.:

515955

Cov.:

AF XY:

0.843

AC XY:

607375

AN XY:

720650

show subpopulations

Gnomad4 AFR exome

AF:

0.473

Gnomad4 AMR exome

AF:

0.682

Gnomad4 ASJ exome

AF:

0.916

Gnomad4 EAS exome

AF:

0.858

Gnomad4 SAS exome

AF:

0.785

Gnomad4 FIN exome

AF:

0.875

Gnomad4 NFE exome

AF:

0.860

Gnomad4 OTH exome

AF:

0.835

GnomAD4 genome

AF:

0.745

AC:

113297

AN:

152046

Hom.:

44288

Cov.:

AF XY:

0.747

AC XY:

55496

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.739

Gnomad4 ASJ

AF:

0.927

Gnomad4 EAS

AF:

0.857

Gnomad4 SAS

AF:

0.761

Gnomad4 FIN

AF:

0.870

Gnomad4 NFE

AF:

0.861

Gnomad4 OTH

AF:

0.791

Alfa

AF:

0.841

Hom.:

93340

Bravo

AF:

0.724

Asia WGS

AF:

0.759

AC:

2639

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

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

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.47

DANN

Benign

0.49

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