Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
FGFR1
Final classification
VUS
FGFR1 c.521C>G · p.Thr174Arg
FGFR1

NM_001174067.1:c.521C>G (p.Thr174Arg) is a missense variant in exon 5 of FGFR1, encoding a substitution of threonine to arginine at codon 174 in the extracellular Ig-like domain.

Gene
FGFR1
Transcript
NM_001174067.1
HGVS · transcript:coding
NM_001174067.1:c.521C>G
Consequence
N/A
GRCh38
chr8:38428372 G>C
GRCh37
chr8:38285890 G>C
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.521C>G

NM_001174067.1:c.521C>G (p.Thr174Arg) is a missense variant in exon 5 of FGFR1, encoding a substitution of threonine to arginine at codon 174 in the extracellular Ig-like domain. This variant is present at very low frequency in population databases: gnomAD v2.1 (27/278,536 alleles, AF=0.0097%) and gnomAD v4.1 (483/1,614,016 alleles, AF=0.03%), meeting PM2 at the supporting level. It is absent from gnomAD-Canada v1.0.1 Computational predictors unanimously suggest a benign or neutral effect: REVEL score is 0.263 (below the pathogenic threshold), BayesDel is −0.147 (benign-leaning), and SpliceAI predicts no splicing impact (max delta 0.01), meeting BP4 at the supporting level.2 OncoKB annotates this variant as Likely Neutral. COSMIC records this variant in two somatic cancer samples (COSV58328267), but no germline functional or case-level evidence of pathogenicity is available.3 ClinVar classifies this variant as Uncertain significance (Variation ID: 1024176) based on three submissions, all with criteria provided at the single-submitter level. No expert panel has reviewed this variant.4 A comprehensive functional screen of 160 FGFR variants (PMID:34272467) did not include Thr174Arg. No variant-specific functional studies have been performed.5 FGFR1 variant classification literature (PMID:37805574) establishes domain-based enrichment for IHH-associated missense variants but does not specifically address the Thr174 residue.6 With PM2_supporting and BP4_supporting both met, the evidence is balanced and insufficient to classify this variant as pathogenic or benign. The variant remains a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines.7

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
      This variant is present in gnomAD v4.1 (AF= 0.000299254; MAF= 0.02993%, 483/1614016 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000432097; MAF= 0.04321%, 27/62486 alleles, homozygotes = 0); grpmax FAF= 0.00035348.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 9.69354e-05; MAF= 0.00969%, 27/278536 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000190027; MAF= 0.01900%, 24/126298 alleles, homozygotes = 0); grpmax FAF= 0.00011951.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.0001085894233901618, 2/18418 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.03% · 483 / 1,614,016
      0 hom · FAF 0.035%
      Remaining individuals
      27 / 62,486
      0.043%
      European (non-Finnish)
      452 / 1,180,030
      0.038%
      African/African American
      3 / 74,924
      0.004%
      Ashkenazi Jewish
      1 / 29,608
      0.0034%
      + 6 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian)
      gnomAD v2.1
      0.0097% · 27 / 278,536
      0 hom · FAF 0.012%
      European (non-Finnish)
      24 / 126,298
      0.019%
      Remaining individuals
      1 / 7,136
      0.014%
      African/African American
      2 / 24,200
      0.0083%
      + 5 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      gnomAD Canada 🇨🇦
      0.011% · 2 / 18,418
      0 hom · FAF 0.003%
      European (non-Finnish)
      2 / 11,738
      0.017%
      + 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      Error retrieving ClinVar entry.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.263. BayesDel score = -0.147005.
      Functional / OncoKB screenshot
      Functional Likely Neutral
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
      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; COSV58328267, 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 · 8 PMIDs not cited in assessment
      34272467 ↗ Comprehensive functional evaluation of variants of fibroblast growth factor receptor genes in cancer. ONCOKB
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      20301509 ↗ Isolated Gonadotropin-Releasing Hormone (GnRH) Deficiency. CLINVAR
      20301628 ↗ FGFR Craniosynostosis Syndromes Overview. CLINVAR
      23533228 ↗ Prioritizing genetic testing in patients with Kallmann syndrome using clinical phenotypes. CLINVAR
      26937548 ↗ FGFR1-Related Hartsfield Syndrome. CLINVAR
      35099867 ↗ Encephalocraniocutaneous Lipomatosis. CLINVAR
      37805574 ↗ How human genetic context can inform pathogenicity classification: FGFR1 variation in idiopathic hypogonadotropic hypogonadism. CLINVAR