5-150117614-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002609.4(PDGFRB):c.3137+4A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 1,557,850 control chromosomes in the GnomAD database, including 131,370 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002609.4 splice_region, intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDGFRB | NM_002609.4 | c.3137+4A>G | splice_region_variant, intron_variant | Intron 22 of 22 | ENST00000261799.9 | NP_002600.1 | ||
PDGFRB | NM_001355016.2 | c.2945+4A>G | splice_region_variant, intron_variant | Intron 21 of 21 | NP_001341945.1 | |||
PDGFRB | NM_001355017.2 | c.2654+4A>G | splice_region_variant, intron_variant | Intron 22 of 22 | NP_001341946.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFRB | ENST00000261799.9 | c.3137+4A>G | splice_region_variant, intron_variant | Intron 22 of 22 | 1 | NM_002609.4 | ENSP00000261799.4 | |||
PDGFRB | ENST00000520579.5 | n.*2451+4A>G | splice_region_variant, intron_variant | Intron 22 of 22 | 1 | ENSP00000430026.1 |
Frequencies
GnomAD3 genomes AF: 0.377 AC: 56810AN: 150874Hom.: 11093 Cov.: 30
GnomAD3 exomes AF: 0.348 AC: 86283AN: 248036Hom.: 16475 AF XY: 0.354 AC XY: 47476AN XY: 134070
GnomAD4 exome AF: 0.406 AC: 570893AN: 1406860Hom.: 120262 Cov.: 24 AF XY: 0.404 AC XY: 283603AN XY: 701714
GnomAD4 genome AF: 0.377 AC: 56855AN: 150990Hom.: 11108 Cov.: 30 AF XY: 0.365 AC XY: 26923AN XY: 73696
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Acroosteolysis-keloid-like lesions-premature aging syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Basal ganglia calcification, idiopathic, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Myofibromatosis, infantile, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Feb 01, 2025 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | - - |
Myeloproliferative disorder, chronic, with eosinophilia Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
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 | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at