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FGFR1
Final classification
VUS
FGFR1 c.475G>A · p.Glu159Lys
FGFR1

PM2 (supporting) is met: NM_001174067.1:c.475G>A is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (allele frequency 0%).

Gene
FGFR1
Transcript
NM_001174067.1
HGVS · transcript:coding
NM_001174067.1:c.475G>A
Consequence
N/A
GRCh38
chr8:38428418 C>T
GRCh37
chr8:38285936 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
FGFR1 c.475G>A

PM2 (supporting) is met: NM_001174067.1:c.475G>A is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (allele frequency 0%).1 BP4 (supporting benign) is met: multiple lines of in silico evidence suggest no deleterious impact, including SpliceAI max delta 0.03 (no splicing effect), BayesDel 0.049 (benign range), and REVEL 0.522 (indeterminate).2 PVS1 is not applicable: c.475G>A is a missense variant (p.Glu159Lys) and does not meet the null-variant criteria required for PVS1 assessment per ClinGen SVI PVS1 recommendations (PMC6185798).3 PS3/BS3 not assessed: no well-established functional studies were identified for this variant. OncoKB reports Unknown Oncogenic Effect.4 PP5/BP6 not assessed: ClinVar submissions were matched to a different variant (NM_023110.3:c.742G>A, p.Val248Met) and all are non-exact matches; no expert panel or reputable source classification exists for this specific variant.5 PS4 not met: variant is rare (absent from gnomAD) but no case-control enrichment data are available to establish statistically significant association with disease.6 PP3 not met: combined in silico evidence (REVEL 0.522, BayesDel 0.049, SpliceAI max delta 0.03) does not support a deleterious effect.7 No publications reviewed (PMIDs: 21082653, 20301509, 20301628, 28492532) mention the specific variant NM_001174067.1:c.475G>A. All are gene-level reviews or methodology papers without variant-specific evidence. Final classification: Uncertain Significance (VUS). One supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met, yielding conflicting evidence that does not meet the threshold for Likely Pathogenic, Likely Benign, Pathogenic, or Benign classification under generic ACMG/AMP 2015 combination rules (PMID:25741868).8

PM2 + BP4 VUS
Gene diagram · NM_001174067.1 · variants mapped to exon structure
FGFR1 NM_001174067.1
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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
      Error retrieving ClinVar entry.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.522. BayesDel score = 0.0494725.
      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. FGFR1, a receptor tyrosine kinase, is altered by mutation, chromosomal rearrangement or amplification in various cancer types including lung and breas
      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
      Triaged references · 4 PMIDs not cited in assessment
      21082653 ↗ Genetic basis of potential therapeutic strategies for craniosynostosis. CLINVAR
      20301509 ↗ Isolated Gonadotropin-Releasing Hormone (GnRH) Deficiency. CLINVAR
      20301628 ↗ FGFR Craniosynostosis Syndromes Overview. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR