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FGFR1
Final classification
VUS
FGFR1 c.2242C>T · p.His748Tyr
FGFR1

NM_001174067.1:c.2242C>T (p.His748Tyr) is a missense variant in exon 17 of FGFR1, encoding the tyrosine kinase domain.

Gene
FGFR1
Transcript
NM_001174067.1
HGVS · transcript:coding
NM_001174067.1:c.2242C>T
Consequence
N/A
GRCh38
chr8:38414189 G>A
GRCh37
chr8:38271707 G>A
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; combination = 1 supporting, 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
FGFR1 c.2242C>T

NM_001174067.1:c.2242C>T (p.His748Tyr) is a missense variant in exon 17 of FGFR1, encoding the tyrosine kinase domain.1 This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), meeting PM2 at a supporting level under generic ACMG/AMP thresholds.2 No other pathogenic or likely pathogenic criteria were met. PVS1 is not applicable (missense, not a null variant). PS1 and PM5 could not be assessed because no pathogenic comparator missense at codon 748 was identified. PS3/BS3 were not met due to absence of variant-specific functional data; OncoKB reports 'Unknown Oncogenic Effect.' PS4 was not met because no case-control or cohort data exist. PP3/BP4 were not met due to equivocal in silico predictions (REVEL 0.648 vs. BayesDel 0.129). PP5/BP6 were not met because no reputable source has classified this specific variant, and the ClinVar match was to a different variant on a different transcript.3 With only one supporting pathogenic criterion (PM2) met and no benign criteria met, the variant does not reach a classifiable tier under ACMG/AMP 2015 combination rules. The evidence is insufficient to classify this variant as pathogenic, likely pathogenic, benign, or likely benign. The variant is therefore a Variant of Uncertain Significance (VUS).4

PM2 VUS
1 pvs1_variant_assessment
3 pvs1_variant_assessmentpm5_candidatesoncokb ↗revelbayesdelclinvar ↗
4 generic_acmg_combination_rules
Gene diagram · NM_001174067.1 · variants mapped to exon structure
FGFR1 NM_001174067.1
Fetching transcript structure from UCSC…
Applied criteria · 1 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 = 0.00). REVEL score = 0.648. BayesDel score = 0.128631.
      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 previously been reported in somatic cancers (COSMIC; COSV58334750, n = 2 times).
      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 · 3 PMIDs not cited in assessment
      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