rs2291591
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006206.6(PDGFRA):c.2323+1120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 1,352,558 control chromosomes in the GnomAD database, including 5,342 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.084 ( 583 hom., cov: 33)
Exomes 𝑓: 0.086 ( 4759 hom. )
Consequence
PDGFRA
NM_006206.6 intron
NM_006206.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.275
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRA | NM_006206.6 | c.2323+1120C>T | intron_variant | ENST00000257290.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.2323+1120C>T | intron_variant | 1 | NM_006206.6 | P1 | |||
PDGFRA | ENST00000507536.1 | n.771C>T | non_coding_transcript_exon_variant | 5/5 | 1 | ||||
PDGFRA | ENST00000509490.5 | c.*266C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0839 AC: 12757AN: 152112Hom.: 582 Cov.: 33
GnomAD3 genomes
AF:
AC:
12757
AN:
152112
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0725 AC: 9713AN: 134042Hom.: 411 AF XY: 0.0711 AC XY: 5192AN XY: 72976
GnomAD3 exomes
AF:
AC:
9713
AN:
134042
Hom.:
AF XY:
AC XY:
5192
AN XY:
72976
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0862 AC: 103495AN: 1200328Hom.: 4759 Cov.: 31 AF XY: 0.0844 AC XY: 49542AN XY: 587084
GnomAD4 exome
AF:
AC:
103495
AN:
1200328
Hom.:
Cov.:
31
AF XY:
AC XY:
49542
AN XY:
587084
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0839 AC: 12769AN: 152230Hom.: 583 Cov.: 33 AF XY: 0.0824 AC XY: 6136AN XY: 74432
GnomAD4 genome
AF:
AC:
12769
AN:
152230
Hom.:
Cov.:
33
AF XY:
AC XY:
6136
AN XY:
74432
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
167
AN:
3478
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Benign:2Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Myeloproliferative neoplasm, unclassifiable Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Dept. of Cytogenetics, ICMR- National Institute of Immunohaematology | Aug 25, 2022 | - - |
PDGFRA-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hereditary cancer Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | Mar 27, 2024 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at