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NF1
Final classification
VUS
NF1 c.6776T>C · p.Val2259Ala
NF1

NM_001042492.2:c.6776T>C (p.Val2259Ala) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).

Gene
NF1
Transcript
NM_001042492.2
HGVS · transcript:coding
NM_001042492.2:c.6776T>C
Consequence
N/A
GRCh38
chr17:31338096 T>C
GRCh37
chr17:29665114 T>C
Basis Neurofibromatosis and Schwannomatosis Specification v1.0.0 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.
Neurofibromatosis and Schwannomatosis Specification v1.0.0 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
NF1 c.6776T>C

NM_001042492.2:c.6776T>C (p.Val2259Ala) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).1 Multiple in silico predictors suggest a neutral effect: REVEL score 0.29, BayesDel score -0.045, and SpliceAI max delta 0.08 (BP4_Supporting).2 ClinVar classifies this variant as Uncertain Significance (VariationID 826571, 1 clinical laboratory, criteria provided, single submitter).3 No variant-specific functional studies, de novo observations, segregation data, or case-control evidence were identified for this variant.4 With PM2 (supporting pathogenic) and BP4 (supporting benign) as the only met criteria, the evidence is insufficient to classify beyond Uncertain Significance. This classification is consistent with the existing ClinVar entry.5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_001042492.2 · variants mapped to exon structure
NF1 NM_001042492.2
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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 826571)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.29. BayesDel score = -0.045496.
      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. NF1, a negative regulator of RAS, is inactivated by mutation or deletion in various solid and hematologic malignancies.
      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; COSV106479531, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 1 PMID not cited in assessment
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR