Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
PDGFRA
Final classification
VUS
PDGFRA c.2524_2526delinsCGA · p.Asp842Arg
PDGFRA

NM_006206.6:c.2524_2526delinsCGA (p.Asp842Arg) in PDGFRA is an in-frame deletion-insertion altering the kinase activation loop residue Asp842, a statistically significant mutational hotspot (PM1). The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2).

Gene
PDGFRA
Transcript
NM_006206.6
HGVS · transcript:coding
NM_006206.6:c.2524_2526delinsCGA
Consequence
N/A
GRCh38
chr4:54285925 GAC>CGA
GRCh37
chr4:55152092 GAC>CGA
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
PDGFRA c.2524_2526delinsCGA

NM_006206.6:c.2524_2526delinsCGA (p.Asp842Arg) in PDGFRA is an in-frame deletion-insertion altering the kinase activation loop residue Asp842, a statistically significant mutational hotspot (PM1). The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2).1 No other pathogenic or likely pathogenic criteria were met. PVS1 is not applicable (in-frame variant, not a null variant). PS3 functional evidence was not established: although D842R is annotated as Likely Oncogenic by OncoKB and lies in a hotspot, no variant-specific reviewed functional data with citations were identified in the literature packet. No segregation, de novo, in silico, or clinical case data were available.2 Under the generic ACMG/AMP 2015 classification framework (PMID:25741868), the combination of two moderate criteria (PM1 + PM2) without additional supporting evidence is insufficient to reach the Likely Pathogenic threshold, which requires ≥3 moderate criteria or ≥2 moderate with ≥2 supporting. The variant is classified as a Variant of Uncertain Significance (VUS).3

PM1 + PM2 VUS
2 pvs1_variant_assessmentoncokb ↗clinvar ↗
3 generic_acmg_combination_rules
Gene diagram · NM_006206.6 · variants mapped to exon structure
PDGFRA NM_006206.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 3 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
The variant alters Asp842 in the activation loop of the PDGFRA tyrosine kinase domain (exon 18). This residue is a statistically significant mutational hotspot (Cancer Hotspots confirmed) and lies within a critical well-established functional domain without benign variation.
Cancer Hotspots: residue D842 is a statistically significant hotspotOncoKB: Likely Oncogeniclocated in kinase activation loop
PM2 moderate Pathogenic
Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (allele frequency 0%), which is below the PM2 threshold of <0.1% for a rare variant in a gene with established disease association.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes/genomes)Absent from gnomAD-Canada v1.0
Assessed · not applied
Pathogenic
PS3 PDGFRA D842R is annotated as Likely Oncogenic (Likely Gain-of-function) by OncoKB and residue Asp842 is a statistically significant cancer hotspot, consistent with a known activating mutation in the kinase activation loop.
Benign
BA1 The variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada).
BS1 The variant is absent from all population databases (allele frequency 0%), which is well below the BS1 threshold of >0.3%.
N/A · 22 PVS1 · PS1 · PS2 · PS4 · PM4 · PM5 · PM6 · PP1 · PP2 · PP3 · PP4 · PP5 · BS2 · BS3 · BS4 · BP1 · BP2 · BP3 · BP4 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico No data
No in-silico prediction was recorded for this variant.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PDGFRA, a receptor tyrosine kinase, is altered by mutation, chromosomal rearrangement or amplification in a diverse range of cancers.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots