rs2307049
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000508170.5(PDGFRA):c.*31G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,502,626 control chromosomes in the GnomAD database, including 19,525 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 2992 hom., cov: 31)
Exomes 𝑓: 0.14 ( 16533 hom. )
Consequence
PDGFRA
ENST00000508170.5 3_prime_UTR
ENST00000508170.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.314
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 made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 4-54263987-G-A is Benign according to our data. Variant chr4-54263987-G-A is described in ClinVar as [Benign]. Clinvar id is 1276038.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRA | NM_006206.6 | c.628+60G>A | intron_variant | ENST00000257290.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000508170.5 | c.*31G>A | 3_prime_UTR_variant | 4/4 | 1 | ||||
PDGFRA | ENST00000257290.10 | c.628+60G>A | intron_variant | 1 | NM_006206.6 | P1 | |||
PDGFRA | ENST00000509490.5 | c.628+60G>A | intron_variant, NMD_transcript_variant | 1 | |||||
PDGFRA | ENST00000509092.5 | n.446+60G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.181 AC: 27392AN: 151540Hom.: 2992 Cov.: 31
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GnomAD3 exomes AF: 0.220 AC: 42546AN: 193732Hom.: 5365 AF XY: 0.207 AC XY: 21987AN XY: 106038
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GnomAD4 exome AF: 0.143 AC: 193429AN: 1350972Hom.: 16533 Cov.: 21 AF XY: 0.143 AC XY: 96731AN XY: 675648
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GnomAD4 genome ? AF: 0.181 AC: 27423AN: 151654Hom.: 2992 Cov.: 31 AF XY: 0.184 AC XY: 13600AN XY: 74058
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 10, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at