Genetic Variant NM_006206.6:c.-13+111dupA (chr4-54229515-G-GA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006206.6(PDGFRA):c.-13+111dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 311,106 control chromosomes in the GnomAD database, including 5,482 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5046 hom., cov: 21)

Exomes 𝑓: 0.27 ( 436 hom. )

Consequence

PDGFRA
NM_006206.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.51

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:

ENSG00000282278 (HGNC:):

ENSG00000282278 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 4-54229515-G-GA is Benign according to our data. Variant chr4-54229515-G-GA is described in ClinVar as [Benign]. Clinvar id is 1257913.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PDGFRA	NM_006206.6 link	c.-13+111dupA	intron_variant	Intron 1 of 22	ENST00000257290.10	NP_006197.1	P16234-1
PDGFRA	NM_001347828.2 link	c.-16+111dupA	intron_variant	Intron 1 of 23		NP_001334757.1
PDGFRA	NM_001347827.2 link	c.-13+111dupA	intron_variant	Intron 1 of 16		NP_001334756.1
PDGFRA	XM_006714041.4 link	c.-16+111dupA	intron_variant	Intron 1 of 17		XP_006714104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFRA	ENST00000257290.10 link	c.-13+111dupA		intron_variant	Intron 1 of 22	1	NM_006206.6	ENSP00000257290.5		P16234-1
ENSG00000282278	ENST00000507166.5 link	c.1018-45399dupA		intron_variant	Intron 12 of 23	2		ENSP00000423325.1		A0A0B4J203

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

37271

AN:

142140

Hom.:

5042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.215

Gnomad MID

AF:

0.151

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.232

GnomAD4 exome

AF:

0.268

AC:

45251

AN:

168920

Hom.:

436

AF XY:

0.266

AC XY:

22817

AN XY:

85728

show subpopulations

African (AFR)

AF:

0.353

AC:

1870

AN:

5290

American (AMR)

AF:

0.358

AC:

1958

AN:

5462

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

1102

AN:

5828

East Asian (EAS)

AF:

0.243

AC:

3746

AN:

15396

South Asian (SAS)

AF:

0.294

AC:

466

AN:

1584

European-Finnish (FIN)

AF:

0.258

AC:

3592

AN:

13898

Middle Eastern (MID)

AF:

0.245

AC:

201

AN:

820

European-Non Finnish (NFE)

AF:

0.267

AC:

29126

AN:

109118

Other (OTH)

AF:

0.277

AC:

3190

AN:

11524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.421

Heterozygous variant carriers

1393

2787

4180

5574

6967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.262

AC:

37306

AN:

142186

Hom.:

5046

Cov.:

AF XY:

0.263

AC XY:

18106

AN XY:

68850

show subpopulations

African (AFR)

AF:

0.351

AC:

13685

AN:

39020

American (AMR)

AF:

0.339

AC:

4887

AN:

14398

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

339

AN:

3316

East Asian (EAS)

AF:

0.203

AC:

992

AN:

4878

South Asian (SAS)

AF:

0.263

AC:

1179

AN:

4484

European-Finnish (FIN)

AF:

0.215

AC:

1756

AN:

8162

Middle Eastern (MID)

AF:

0.157

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.214

AC:

13848

AN:

64816

Other (OTH)

AF:

0.232

AC:

455

AN:

1962

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1284

2568

3851

5135

6419

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0584

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Aug 30, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.5

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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NM_006206.6:c.-13+111dupA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over