4-54229515-G-GA

Variant names:

• chr4-54229515-G-GA
• rs565335773
• NM_006206.6:c.-13+111dupA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51

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]

ENSG00000282278 (HGNC:):

ACMG classification

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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFRA	NM_006206.6	c.-13+111dupA		intron_variant	Intron 1 of 22	ENST00000257290.10	NP_006197.1
PDGFRA	NM_001347828.2	c.-16+111dupA		intron_variant	Intron 1 of 23		NP_001334757.1
PDGFRA	NM_001347827.2	c.-13+111dupA		intron_variant	Intron 1 of 16		NP_001334756.1
PDGFRA	XM_006714041.4	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	c.-13+111dupA		intron_variant	Intron 1 of 22	1	NM_006206.6	ENSP00000257290.5
ENSG00000282278	ENST00000507166.5	c.1018-45399dupA		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 37271 AN: 142140 Hom.: 5042 Cov.: 21

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

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

GnomAD4 genome AF: 0.262 AC: 37306 AN: 142186 Hom.: 5046 Cov.: 21 AF XY: 0.263 AC XY: 18106 AN XY: 68850

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: 43 AN: 274

European-Non Finnish (NFE) AF: 0.214 AC: 13848 AN: 64816

Other (OTH) AF: 0.232 AC: 455 AN: 1962

Alfa AF: 0.0584 Hom.: 67

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 30, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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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Other links and lift over

dbSNP: rs565335773; hg19: chr4-55095682; COSMIC: COSV57275750; COSMIC: COSV57275750;