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FGFR1
Final classification
VUS
PM2
FGFR1
c.2242C>T
p.His748Tyr
This variant

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

Transcript
NM_001174067.1
HGVS · transcript:coding
NM_001174067.1:c.2242C>T
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 applied · 21 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). Under generic ACMG/AMP thresholds, complete absence from population databases supports PM2 at a supporting level (allele frequency <0.1% for dominant disorders).
Absent from gnomAD v2.1.Absent from gnomAD v4.1.Absent from gnomAD-Canada v1.0.
Assessed · not applied · 21 not met · 0 not assessed
Pathogenic
PS1 No evidence that a different missense change at the same codon (His748) has been established as pathogenic.
PS2 No de novo observation reported for this variant.
PS3 No well-established functional studies demonstrating a deleterious effect were identified for this variant.
PS4 No case-control data demonstrating enrichment of this variant in affected individuals versus controls.
PM1 This variant (p.His748Tyr) is not located in a statistically significant mutational hotspot.
PM6 No de novo observation without confirmation of paternity and maternity is reported for this variant.
PP1 No cosegregation data are available for this variant.
PP2 PP2 requires a gene with a low rate of benign missense variation where missense variants are a common disease mechanism.
PP3 In silico predictions are equivocal.
PP4 No patient phenotype or family history data were provided.
PP5 No reputable source has classified this specific variant (NM_001174067.1:c.2242C>T) as pathogenic.
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No data are available demonstrating observation of this variant in a healthy adult individual for a fully penetrant dominant disorder.
BS3 No well-established functional studies demonstrating no deleterious effect were identified for this variant.
BS4 No cosegregation data are available to demonstrate lack of segregation with disease.
BP1 BP1 applies when a missense variant occurs in a gene where only truncating variants cause disease.
BP2 No data are available regarding observation of this variant in trans with a known pathogenic variant.
BP4 In silico predictions are equivocal.
BP5 No evidence was found that this variant was observed in a case with an alternative molecular cause for disease.
BP6 No reputable source has classified this specific variant (NM_001174067.1:c.2242C>T) as benign or likely 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 = 0.00). 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