ENST00000508170.5:c.*31G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000508170.5(PDGFRA):c.*31G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,502,626 control chromosomes in the GnomAD database, including 19,525 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2992 hom., cov: 31)

Exomes 𝑓: 0.14 ( 16533 hom. )

Consequence

PDGFRA
ENST00000508170.5 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.314

Publications

11 publications found

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 Gene-Disease associations (from GenCC):

gastrointestinal stromal tumor
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
polyps, multiple and recurrent inflammatory fibroid, gastrointestinal
Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P
congenital heart disease
Inheritance: AD Classification: LIMITED Submitted by: ClinGen
isolated cleft palate
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

PDGFRA links:

ENSG00000282278 (HGNC:):

ENSG00000282278 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 4-54263987-G-A is Benign according to our data. Variant chr4-54263987-G-A is described in ClinVar as Benign. ClinVar VariationId is 1276038.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508170.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PDGFRA	NM_006206.6	MANE Select	c.628+60G>A	intron	N/A	NP_006197.1
PDGFRA	NM_001347828.2		c.703+60G>A	intron	N/A	NP_001334757.1
PDGFRA	NM_001347830.2		c.667+60G>A	intron	N/A	NP_001334759.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PDGFRA	ENST00000508170.5	TSL:1	c.*31G>A	3_prime_UTR	Exon 4 of 4	ENSP00000425648.1
PDGFRA	ENST00000257290.10	TSL:1 MANE Select	c.628+60G>A	intron	N/A	ENSP00000257290.5
ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-10938G>A	intron	N/A	ENSP00000423325.1

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27392

AN:

151540

Hom.:

2992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.0703

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.155

GnomAD2 exomes

AF:

0.220

AC:

42546

AN:

193732

AF XY:

0.207

show subpopulations

Gnomad AFR exome

AF:

0.282

Gnomad AMR exome

AF:

0.453

Gnomad ASJ exome

AF:

0.0834

Gnomad EAS exome

AF:

0.209

Gnomad FIN exome

AF:

0.149

Gnomad NFE exome

AF:

0.143

Gnomad OTH exome

AF:

0.176

GnomAD4 exome

AF:

0.143

AC:

193429

AN:

1350972

Hom.:

16533

Cov.:

AF XY:

0.143

AC XY:

96731

AN XY:

675648

show subpopulations

African (AFR)

AF:

0.255

AC:

7758

AN:

30382

American (AMR)

AF:

0.418

AC:

17095

AN:

40908

Ashkenazi Jewish (ASJ)

AF:

0.0776

AC:

1929

AN:

24856

East Asian (EAS)

AF:

0.167

AC:

6487

AN:

38846

South Asian (SAS)

AF:

0.228

AC:

18098

AN:

79308

European-Finnish (FIN)

AF:

0.121

AC:

5082

AN:

41892

Middle Eastern (MID)

AF:

0.100

AC:

543

AN:

5418

European-Non Finnish (NFE)

AF:

0.124

AC:

128174

AN:

1032766

Other (OTH)

AF:

0.146

AC:

8263

AN:

56596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

7543

15086

22629

30172

37715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4818

9636

14454

19272

24090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.181

AC:

27423

AN:

151654

Hom.:

2992

Cov.:

AF XY:

0.184

AC XY:

13600

AN XY:

74058

show subpopulations

African (AFR)

AF:

0.254

AC:

10504

AN:

41320

American (AMR)

AF:

0.290

AC:

4422

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.0703

AC:

244

AN:

3472

East Asian (EAS)

AF:

0.184

AC:

947

AN:

5158

South Asian (SAS)

AF:

0.247

AC:

1181

AN:

4790

European-Finnish (FIN)

AF:

0.126

AC:

1319

AN:

10456

Middle Eastern (MID)

AF:

0.0548

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.123

AC:

8384

AN:

67896

Other (OTH)

AF:

0.154

AC:

324

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1072

2144

3216

4288

5360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

286

572

858

1144

1430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.138

Hom.:

2458

Bravo

AF:

0.195

Asia WGS

AF:

0.244

AC:

844

AN:

3466

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Aug 10, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

(source)

DANN

Benign

0.58

PhyloP100

-0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over