rs41287108
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4BP6_Very_StrongBP7BS1BS2
The NM_002609.4(PDGFRB):c.2523G>A(p.Lys841Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00343 in 1,613,974 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002609.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PDGFRB | NM_002609.4 | c.2523G>A | p.Lys841Lys | synonymous_variant | Exon 18 of 23 | ENST00000261799.9 | NP_002600.1 | |
PDGFRB | NM_001355016.2 | c.2331G>A | p.Lys777Lys | synonymous_variant | Exon 17 of 22 | NP_001341945.1 | ||
PDGFRB | NM_001355017.2 | c.2040G>A | p.Lys680Lys | synonymous_variant | Exon 18 of 23 | NP_001341946.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00243 AC: 369AN: 152160Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00309 AC: 777AN: 251468Hom.: 4 AF XY: 0.00349 AC XY: 475AN XY: 135918
GnomAD4 exome AF: 0.00353 AC: 5164AN: 1461696Hom.: 27 Cov.: 32 AF XY: 0.00369 AC XY: 2683AN XY: 727164
GnomAD4 genome AF: 0.00243 AC: 370AN: 152278Hom.: 2 Cov.: 32 AF XY: 0.00240 AC XY: 179AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:6
This variant is associated with the following publications: (PMID: 27535533) -
PDGFRB: BP4, BS2 -
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not specified Benign:1
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PDGFRB-related disorder Benign:1
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). -
Myofibromatosis, infantile, 1 Benign:1
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Myeloproliferative disorder, chronic, with eosinophilia Benign:1
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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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at