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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 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_213647.2:c.317C>T is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases (allele frequency < 0.1%), meeting the PM2 criterion for a variant absent or at extremely low frequency in large population cohorts.
gnomAD v2.1: absentgnomAD v4.1: absentgnomAD-Canada: absent (AC=0
BP4 supporting Benign
Multiple lines of in silico evidence suggest no significant impact on gene product. BayesDel score is -0.025 (benign range), SpliceAI max delta is 0.00 (no predicted splice alteration), and REVEL score is 0.43 (below accepted pathogenicity thresholds). Together these predictors favor a neutral or minimally disruptive effect.
REVEL: 0.43 (below typical pathogenic threshold)BayesDel: -0.025 (benign-leaning)SpliceAI: max delta 0.00 (no splice impact)
Assessed · not applied
Pathogenic
PS1 No alternate nucleotide change producing the same amino acid substitution (p.Ser106Phe) has been identified as pathogenic in ClinVar or the literature.
PS2 No de novo observation for NM_213647.2:c.317C>T was identified.
PS3 No well-established in vitro or in vivo functional studies were identified for NM_213647.2:c.317C>T (p.Ser106Phe).
PS4 No case-control or statistical enrichment data are available for NM_213647.2:c.317C>T.
PM1 NM_213647.2:c.317C>T (p.Ser106Phe) is located in the extracellular immunoglobulin-like domain of FGFR4, but does not lie in a statistically significant mutational hotspot per cancerhotspots.org, and no germline disease-associated mutational hotspot encompassing codon 106 has been established for FGFR4.
PM6 No de novo observation with confirmed maternity and paternity was identified for NM_213647.2:c.317C>T.
PP1 No co-segregation data are available for NM_213647.2:c.317C>T.
PP2 HCI prior scores are unavailable for FGFR4, and no gene-level missense constraint metric (e.g., missense Z-score) is available from the evidence pipeline.
PP3 In silico predictors do not provide multiple lines of evidence supporting a deleterious effect.
PP4 No proband phenotype or clinical data are available for NM_213647.2:c.317C>T.
PP5 NM_213647.2:c.317C>T is absent from ClinVar and has not been classified by any reputable clinical laboratory or expert panel.
Benign
BA1 NM_213647.2:c.317C>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 NM_213647.2:c.317C>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No data are available regarding observation of NM_213647.2:c.317C>T in healthy adults.
BS3 No well-established in vitro or in vivo functional studies demonstrating no deleterious effect of NM_213647.2:c.317C>T (p.Ser106Phe) were identified.
BS4 No segregation data are available to evaluate lack of segregation with disease.
BP1 Although FGFR4 loss-of-function is supported as a disease mechanism by targeted literature review (PMID:26186299, PMID:29735309, PMID:36973520, PMID:19863427, PMID:23880303), there is insufficient evidence that FGFR4-associated disease is caused exclusively by truncating variants such that BP1 would apply to a missense variant.
BP2 No data are available regarding observation of NM_213647.2:c.317C>T in trans with a pathogenic dominant variant.
BP5 No data are available regarding observation of NM_213647.2:c.317C>T in a case with an alternative molecular cause for disease.
BP6 NM_213647.2:c.317C>T is absent from ClinVar and has not been classified as benign by any reputable source.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · 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
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