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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 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_001174067.1:c.475G>A is absent from all population databases: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Allele frequency is 0% in all populations, meeting the non-VCEP PM2 threshold of <0.1%.
Absent from gnomAD v2.1 (exomes)gnomAD v4.1 (exomes/genomes)and gnomAD-Canada v1.0. Allele count = 0 across all populations.
BP4 supporting Benign
Multiple lines of computational evidence suggest no deleterious impact. SpliceAI predicts no splicing impact (max delta score 0.03, well below 0.1 threshold). BayesDel score of 0.049 is strongly in the benign range (well below ~0.27 pathogenic threshold). REVEL score of 0.522 is indeterminate but below the typical 0.7 threshold for pathogenic prediction. The preponderance of in silico evidence supports a benign interpretation.
SpliceAI max delta 0.03 (no splicing impact). BayesDel 0.049 (benign range). REVEL 0.522 (indeterminate). Combined in silico evidence suggests no impact on gene product.
Assessed · not applied
Pathogenic
PS1 No data available on a known pathogenic variant with the same amino acid change at the same residue (Glu159).
PS2 No de novo observation data available for this variant.
PS3 No well-established in vitro or in vivo functional studies were identified for this variant.
PS4 The variant is absent from all population databases (gnomAD v2.1, v4.1, Canada), indicating rarity, but no case-control enrichment data or cohort prevalence data are available to establish statistically significant enrichment in affected individuals.
PM1 PM1 requires location in a mutational hot spot or critical functional domain without benign variation.
PM6 No de novo data available for this variant.
PP1 No segregation data available for this variant.
PP2 PP2 is applicable when a missense variant occurs in a gene with a low rate of benign missense variation and where missense variants are a common disease mechanism.
PP3 Multiple lines of in silico evidence do not support a deleterious effect.
PP4 No variant-specific phenotype or clinical data for the proband are available.
PP5 No reputable source has classified this variant as pathogenic.
Benign
BA1 The variant is absent from all population databases (gnomAD v2.1, v4.1, Canada).
BS1 The variant is absent from all population databases (gnomAD v2.1, v4.1, Canada).
BS2 BS2 requires observation of the variant in a healthy adult individual for a fully penetrant disorder.
BS3 No well-established in vitro or in vivo functional studies demonstrate no damaging effect on protein function or splicing for this variant.
BS4 No segregation data are available to assess lack of cosegregation with disease.
BP1 BP1 applies to missense variants in genes where only truncating variants are a known disease mechanism.
BP2 BP2 requires observation of this variant in trans with a known pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder.
BP5 BP5 requires observation of this variant in a case with an alternate molecular basis for disease.
BP6 BP6 requires a reputable source to classify the variant as benign.
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
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