Starting
Initialising…
0%
FGFR4
Final classification
VUS
FGFR4 c.317C>T · p.Ser106Phe
FGFR4

NM_213647.2:c.317C>T (p.Ser106Phe) is absent from all queried population databases (gnomAD v2.1, v4.1, and gnomAD-Canada), meeting PM2 at moderate strength.

Gene
FGFR4
Transcript
NM_213647.2
HGVS · transcript:coding
NM_213647.2:c.317C>T
Consequence
N/A
GRCh38
chr5:177090615 C>T
GRCh37
chr5:176517616 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 moderate, BP4 supporting benign; combination = 1 moderate + 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
FGFR4 c.317C>T

NM_213647.2:c.317C>T (p.Ser106Phe) is absent from all queried population databases (gnomAD v2.1, v4.1, and gnomAD-Canada), meeting PM2 at moderate strength.1 Multiple in silico predictors suggest no significant impact on the gene product: BayesDel score is -0.025 (benign range), SpliceAI max delta is 0.00, and REVEL score of 0.43 falls below standard pathogenicity thresholds, meeting BP4 at supporting benign strength.2 The variant is absent from ClinVar and the literature; no functional, segregation, de novo, case-control, or clinical classification data are available to assess PS1–PS5, PM6, PP1–PP5, BS2–BS4, BP2, BP5, or BP6.3 PVS1 is not applicable: c.317C>T is a missense variant encoding p.Ser106Phe and does not fall into any null-variant bucket under the ClinGen SVI PVS1 decision tree (PMC6185798).4 PM1 is not met: residue 106 is not a statistically significant mutational hotspot and FGFR4 lacks a germline disease-associated hotspot map. PM5 is not applicable: no same-residue pathogenic comparator variant at codon 106 with a different amino acid change was identified in ClinVar.5 BP1 is not met: while FGFR4 loss-of-function is supported as a disease mechanism by gene-level literature, the gene-disease validity has not been established at a ClinGen level and missense variants are not excluded as a disease mechanism.6 The evidence profile consists of one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4), resulting in conflicting evidence. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), this is classified as a Variant of Uncertain Significance (VUS).7

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 pm5_candidates
6 pvs1_gene_context
7 generic_acmg_combination_rules
Gene diagram · NM_213647.2 · variants mapped to exon structure
FGFR4 NM_213647.2
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
      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 = 0.43. BayesDel score = -0.0252428.
      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. FGFR4, a receptor tyrosine kinase, is altered by mutation, chromosomal rearrangement or amplification at low frequencies in various cancer types.
      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