chr4-54229560-A-ATT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_006206.6(PDGFRA):c.-13+155_-13+156dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000339 in 324,898 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 0.0000067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000057 ( 0 hom. )
Consequence
PDGFRA
NM_006206.6 intron
NM_006206.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.284
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]
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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 | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PDGFRA | NM_006206.6 | c.-13+155_-13+156dupTT | intron_variant | Intron 1 of 22 | ENST00000257290.10 | NP_006197.1 | ||
| PDGFRA | NM_001347828.2 | c.-16+155_-16+156dupTT | intron_variant | Intron 1 of 23 | NP_001334757.1 | |||
| PDGFRA | NM_001347827.2 | c.-13+155_-13+156dupTT | intron_variant | Intron 1 of 16 | NP_001334756.1 | |||
| PDGFRA | XM_006714041.4 | c.-16+155_-16+156dupTT | 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+155_-13+156dupTT | intron_variant | Intron 1 of 22 | 1 | NM_006206.6 | ENSP00000257290.5 | |||
| ENSG00000282278 | ENST00000507166.5 | c.1018-45355_1018-45354dupTT | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 |
Frequencies
GnomAD3 genomes 0.00000672 AC: 1AN: 148732Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
148732
Hom.:
Cov.:
31
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: 0.0000568 AC: 10AN: 176166Hom.: 0 AF XY: 0.0000224 AC XY: 2AN XY: 89254 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
10
AN:
176166
Hom.:
AF XY:
AC XY:
2
AN XY:
89254
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
5208
American (AMR)
AF:
AC:
2
AN:
5368
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
6480
East Asian (EAS)
AF:
AC:
1
AN:
16710
South Asian (SAS)
AF:
AC:
0
AN:
1556
European-Finnish (FIN)
AF:
AC:
0
AN:
15104
Middle Eastern (MID)
AF:
AC:
0
AN:
934
European-Non Finnish (NFE)
AF:
AC:
7
AN:
113120
Other (OTH)
AF:
AC:
0
AN:
11686
⚠️ 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: 0.225
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000672 AC: 1AN: 148732Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72432 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
148732
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
72432
show subpopulations
African (AFR)
AF:
AC:
1
AN:
40592
American (AMR)
AF:
AC:
0
AN:
14882
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3432
East Asian (EAS)
AF:
AC:
0
AN:
5130
South Asian (SAS)
AF:
AC:
0
AN:
4718
European-Finnish (FIN)
AF:
AC:
0
AN:
9744
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66996
Other (OTH)
AF:
AC:
0
AN:
2022
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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