chr5-150115796-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002609.4(PDGFRB):c.3288G>A(p.Ala1096=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,611,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
PDGFRB
NM_002609.4 synonymous
NM_002609.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.236
Genes affected
PDGFRB (HGNC:8804): (platelet derived growth factor receptor beta) The protein encoded by this gene is 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 (PDGFB or PDGFD) or a heterodimer (PDGFA and PDGFB). This gene is essential for normal development of the cardiovascular system and aids in rearrangement of the actin cytoskeleton. This gene is flanked on chromosome 5 by the genes for granulocyte-macrophage colony-stimulating factor and macrophage-colony stimulating factor receptor; all three genes may be implicated in the 5-q syndrome. A translocation between chromosomes 5 and 12, that fuses this gene to that of the ETV6 gene, results in chronic myeloproliferative disorder with eosinophilia. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 5-150115796-C-T is Benign according to our data. Variant chr5-150115796-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2140980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.236 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000138 (21/152206) while in subpopulation AFR AF= 0.000386 (16/41450). AF 95% confidence interval is 0.000241. There are 0 homozygotes in gnomad4. There are 11 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRB | NM_002609.4 | c.3288G>A | p.Ala1096= | synonymous_variant | 23/23 | ENST00000261799.9 | |
PDGFRB | NM_001355016.2 | c.3096G>A | p.Ala1032= | synonymous_variant | 22/22 | ||
PDGFRB | NM_001355017.2 | c.2805G>A | p.Ala935= | synonymous_variant | 23/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRB | ENST00000261799.9 | c.3288G>A | p.Ala1096= | synonymous_variant | 23/23 | 1 | NM_002609.4 | P1 | |
PDGFRB | ENST00000520579.5 | c.*2602G>A | 3_prime_UTR_variant, NMD_transcript_variant | 23/23 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152206Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247560Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134126
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459102Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 725670
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
PDGFRB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 07, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Infantile myofibromatosis;C1866182:Acroosteolysis-keloid-like lesions-premature aging syndrome;C3554321:Basal ganglia calcification, idiopathic, 4;C4225270:Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 02, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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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