chr4-54229515-GAA-G
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_006206.6(PDGFRA):c.-13+110_-13+111delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000479 in 319,746 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: 𝑓 0.000014 ( 0 hom., cov: 21)
Exomes 𝑓: 0.00085 ( 0 hom. )
Consequence
PDGFRA
NM_006206.6 intron
NM_006206.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.184
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 was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PDGFRA | NM_006206.6 | c.-13+110_-13+111delAA | intron_variant | Intron 1 of 22 | ENST00000257290.10 | NP_006197.1 | ||
| PDGFRA | NM_001347828.2 | c.-16+110_-16+111delAA | intron_variant | Intron 1 of 23 | NP_001334757.1 | |||
| PDGFRA | NM_001347827.2 | c.-13+110_-13+111delAA | intron_variant | Intron 1 of 16 | NP_001334756.1 | |||
| PDGFRA | XM_006714041.4 | c.-16+110_-16+111delAA | 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+110_-13+111delAA | intron_variant | Intron 1 of 22 | 1 | NM_006206.6 | ENSP00000257290.5 | |||
| ENSG00000282278 | ENST00000507166.5 | c.1018-45400_1018-45399delAA | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 |
Frequencies
GnomAD3 genomes 0.0000141 AC: 2AN: 142296Hom.: 0 Cov.: 21 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
142296
Hom.:
Cov.:
21
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:
GnomAD4 exome AF: 0.000851 AC: 151AN: 177406Hom.: 0 AF XY: 0.000822 AC XY: 74AN XY: 90058 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
151
AN:
177406
Hom.:
AF XY:
AC XY:
74
AN XY:
90058
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
4
AN:
5436
American (AMR)
AF:
AC:
3
AN:
5652
Ashkenazi Jewish (ASJ)
AF:
AC:
8
AN:
6190
East Asian (EAS)
AF:
AC:
19
AN:
16198
South Asian (SAS)
AF:
AC:
0
AN:
1650
European-Finnish (FIN)
AF:
AC:
16
AN:
14570
Middle Eastern (MID)
AF:
AC:
1
AN:
882
European-Non Finnish (NFE)
AF:
AC:
84
AN:
114860
Other (OTH)
AF:
AC:
16
AN:
11968
⚠️ 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: 0.237
Heterozygous variant carriers
0
25
51
76
102
127
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000141 AC: 2AN: 142340Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 68928 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
2
AN:
142340
Hom.:
Cov.:
21
AF XY:
AC XY:
0
AN XY:
68928
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
39072
American (AMR)
AF:
AC:
0
AN:
14410
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3320
East Asian (EAS)
AF:
AC:
0
AN:
4884
South Asian (SAS)
AF:
AC:
0
AN:
4490
European-Finnish (FIN)
AF:
AC:
2
AN:
8184
Middle Eastern (MID)
AF:
AC:
0
AN:
274
European-Non Finnish (NFE)
AF:
AC:
0
AN:
64864
Other (OTH)
AF:
AC:
0
AN:
1966
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 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: 0.250
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.