Variant rs28489067 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.1121+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,592,174 control chromosomes in the GnomAD database, including 20,333 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2862 hom., cov: 32)

Exomes 𝑓: 0.14 ( 17471 hom. )

Consequence

PDGFRA
NM_006206.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.929

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=-0.63).

BP6

Variant 4-54267769-C-T is Benign according to our data. Variant chr4-54267769-C-T is described in ClinVar as [Benign]. Clinvar id is 259948.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.276 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.1121+28C>T		intron_variant		ENST00000257290.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
PDGFRA	ENST00000257290.10 linkuse as main transcript	c.1121+28C>T	intron_variant	1	NM_006206.6	P1	P16234-1
PDGFRA	ENST00000509490.5 linkuse as main transcript	c.1121+28C>T	intron_variant, NMD_transcript_variant	1			P16234-3
PDGFRA	ENST00000509092.5 linkuse as main transcript	n.939+28C>T	intron_variant, non_coding_transcript_variant	1

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26956

AN:

151944

Hom.:

2860

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.0643

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.184

AC:

45021

AN:

244462

Hom.:

5519

AF XY:

0.175

AC XY:

23255

AN XY:

133224

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.408

Gnomad ASJ exome

AF:

0.0658

Gnomad EAS exome

AF:

0.179

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.119

Gnomad OTH exome

AF:

0.144

GnomAD4 exome

AF:

0.143

AC:

205980

AN:

1440112

Hom.:

17471

Cov.:

AF XY:

0.143

AC XY:

102349

AN XY:

717736

show subpopulations

Gnomad4 AFR exome

AF:

0.248

Gnomad4 AMR exome

AF:

0.393

Gnomad4 ASJ exome

AF:

0.0711

Gnomad4 EAS exome

AF:

0.167

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.144

GnomAD4 genome

AF:

0.177

AC:

26986

AN:

152062

Hom.:

2862

Cov.:

AF XY:

0.180

AC XY:

13372

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.248

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.0643

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.135

Hom.:

325

Bravo

AF:

0.192

Asia WGS

AF:

0.240

AC:

834

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.94

DANN

Benign

0.81

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

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