Genetic Variant PDGFRA:c.-13+109_-13+111dupAAA (chr4-54229515-G-GAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006206.6(PDGFRA):c.-13+109_-13+111dupAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000443 in 180,450 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 21)

Exomes 𝑓: 0.000044 ( 0 hom. )

Consequence

PDGFRA
NM_006206.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PDGFRA	NM_006206.6 link	c.-13+109_-13+111dupAAA	intron_variant	Intron 1 of 22	ENST00000257290.10	NP_006197.1	P16234-1
PDGFRA	NM_001347828.2 link	c.-16+109_-16+111dupAAA	intron_variant	Intron 1 of 23		NP_001334757.1
PDGFRA	NM_001347827.2 link	c.-13+109_-13+111dupAAA	intron_variant	Intron 1 of 16		NP_001334756.1
PDGFRA	XM_006714041.4 link	c.-16+109_-16+111dupAAA	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+109_-13+111dupAAA		intron_variant	Intron 1 of 22	1	NM_006206.6	ENSP00000257290.5		P16234-1
ENSG00000282278	ENST00000507166.5 link	c.1018-45401_1018-45399dupAAA		intron_variant	Intron 12 of 23	2		ENSP00000423325.1		A0A0B4J203

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000443

AC:

AN:

180450

Hom.:

AF XY:

0.0000327

AC XY:

AN XY:

91628

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000181

AC:

AN:

5514

American (AMR)

AF:

0.000350

AC:

AN:

5708

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6346

East Asian (EAS)

AF:

0.000121

AC:

AN:

16522

South Asian (SAS)

AF:

0.00

AC:

AN:

1672

European-Finnish (FIN)

AF:

0.0000675

AC:

AN:

14820

Middle Eastern (MID)

AF:

0.00

AC:

AN:

892

European-Non Finnish (NFE)

AF:

0.00000856

AC:

AN:

116796

Other (OTH)

AF:

0.0000821

AC:

AN:

12180

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.287

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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4-54229515-G-GAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

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