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PDGFRA
Final classification
VUS
PDGFRA c.1988C>T · p.Ala663Val
PDGFRA

NM_006206.5:c.1988C>T (p.Ala663Val) is a missense variant in exon 14 of PDGFRA, a receptor tyrosine kinase gene.

Gene
PDGFRA
Transcript
NM_006206.5
HGVS · transcript:coding
NM_006206.5:c.1988C>T
Consequence
N/A
GRCh38
chr4:54277992 C>T
GRCh37
chr4:55144159 C>T
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: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
PDGFRA c.1988C>T

NM_006206.5:c.1988C>T (p.Ala663Val) is a missense variant in exon 14 of PDGFRA, a receptor tyrosine kinase gene. This variant is absent from gnomAD v2.1 and v4.1 (0/1,607,834 alleles), meeting PM2 at supporting strength.1 In silico analysis yields conflicting predictions: REVEL score of 0.755 suggests a damaging effect, but BayesDel (0.21064) and SpliceAI (max delta 0.00) predict a benign/no-impact outcome. Multiple lines of computational evidence do not converge on pathogenicity; PP3 is not met.2 BayesDel and SpliceAI independently predict no deleterious effect, meeting BP4 at supporting benign strength.3 This variant is absent from ClinVar; no pathogenic or benign classification exists from any expert panel or clinical laboratory. PS1, PS5, PM5, PP5, and BP6 cannot be applied.4 No functional studies, de novo reports, case-control data, segregation data, or publications mentioning this specific variant were identified. PS2, PS3, PS4, PM6, PP1, PP4, BS2, BS3, BS4, BP2, and BP5 are not met.5 The variant is not located in a statistically significant mutational hotspot and no domain-level enrichment data support PM1. The gene-level PVS1 review does not provide robust evidence that PDGFRA disease is primarily caused by truncating variants; BP1 is not met. PVS1 is not applicable to this missense variant.6 PM2 (supporting pathogenic) and BP4 (supporting benign) are both met; the evidence is balanced and does not reach a classification threshold in either direction.7 Using the generic ACMG/AMP 2015 combination rules (Richards et al., PMID:25741868), one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) result in a Variant of Uncertain Significance (VUS).8

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
3 bayesdelspliceai ↗
6 pvs1_variant_assessmentpvs1_gene_context
8 generic_acmg_combination_rules
Gene diagram · NM_006206.5 · variants mapped to exon structure
PDGFRA NM_006206.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 (exomes) and gnomAD v4.1 (0/1,607,834 alleles), meeting the allele frequency threshold for PM2 supporting (<0.1% in population databases).
gnomAD v2.1: absent. gnomAD v4.1: 0/1607834 alleles (AF=0.00%). Absent across all subpopulations.
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on gene product. BayesDel predicts a benign score (0.21064, below the 0.3 threshold). SpliceAI predicts no splicing impact (max delta score = 0.00). Two independent in silico tools converge on a neutral/benign prediction.
BayesDel: 0.21064 (benignbelow 0.3 threshold). SpliceAI: max delta 0.00 (no predicted splice impact). Two independent lines of computational evidence suggest no deleterious effect.
Assessed · not applied
Pathogenic
PS1 No other nucleotide change at this position (p.Ala663) has been reported as pathogenic.
PS2 No de novo evidence (with confirmed paternity/maternity) is available for this variant.
PS3 No well-established in vitro or in vivo functional studies supporting a damaging effect have been identified for this variant.
PS4 No case-control or cohort data demonstrate significantly increased prevalence of this variant in affected individuals compared to controls.
PM1 This variant does not lie in a statistically significant mutational hotspot (cancerhotspots.org).
PM5 No different missense change at codon 663 has been reported as pathogenic.
PM6 No de novo occurrence data (without confirmation of paternity/maternity) are available for this variant.
PP1 No co-segregation data are available for this variant.
PP2 No gene-level constraint metrics (z-score, missense constraint) are available for PDGFRA in the evidence set.
PP3 In silico evidence is conflicting.
PP4 No patient phenotype or family history information is available to assess phenotype specificity.
PP5 This variant is absent from ClinVar.
Benign
BA1 This variant is absent from gnomAD (0/1,607,834 alleles in v4.1).
BS1 This variant is absent from gnomAD (0/1,607,834 alleles in v4.1).
BS2 No data on observation in healthy adults are available.
BS3 No well-established in vitro or in vivo functional studies show no deleterious effect for this variant.
BS4 No segregation data are available for this variant.
BP1 The gene-level PVS1 context review identified papers mentioning PDGFRA, but these papers do not establish that PDGFRA disease is primarily caused by truncating variants.
BP2 No data on observation in trans with a pathogenic variant are available.
BP5 No evidence of an alternate molecular basis for disease in a case harboring this variant is available.
BP6 This variant is absent from ClinVar.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1607834 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74866 alleles, homozygotes = 0).
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 / 1,607,834
0 hom
Not observed in any ancestry group.
+ 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
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
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.755. BayesDel score = 0.21064.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
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 Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots