5-150129831-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002609.4(PDGFRB):c.1505G>A(p.Arg502Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,614,114 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R502W) has been classified as Likely benign.
Frequency
Consequence
NM_002609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRB | NM_002609.4 | c.1505G>A | p.Arg502Gln | missense_variant | 10/23 | ENST00000261799.9 | |
PDGFRB | NM_001355016.2 | c.1313G>A | p.Arg438Gln | missense_variant | 9/22 | ||
PDGFRB | NM_001355017.2 | c.1022G>A | p.Arg341Gln | missense_variant | 10/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRB | ENST00000261799.9 | c.1505G>A | p.Arg502Gln | missense_variant | 10/23 | 1 | NM_002609.4 | P1 | |
PDGFRB | ENST00000520579.5 | c.*819G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/23 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00156 AC: 237AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00198 AC: 498AN: 251254Hom.: 4 AF XY: 0.00182 AC XY: 247AN XY: 135890
GnomAD4 exome AF: 0.00210 AC: 3067AN: 1461740Hom.: 5 Cov.: 33 AF XY: 0.00203 AC XY: 1473AN XY: 727182
GnomAD4 genome AF: 0.00156 AC: 237AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.00153 AC XY: 114AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | PDGFRB: BS1, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
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 | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at