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NF1
Final classification
VUS
NF1 c.3479G>A · p.Gly1160Asp
NF1

NM_001042492.2:c.3479G>A (p.Gly1160Asp) in NF1 is a missense variant absent from gnomAD population databases (v2.1, v4.1, Canada v1.0), satisfying PM2 at supporting strength.

Gene
NF1
Transcript
NM_001042492.2
HGVS · transcript:coding
NM_001042492.2:c.3479G>A
Consequence
N/A
GRCh38
chr17:31232864 G>A
GRCh37
chr17:29559882 G>A
Basis ClinGen Neurofibromatosis and Schwannomatosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NF1 Version 1.0 v1.0 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.
ClinGen Neurofibromatosis and Schwannomatosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NF1 Version 1.0 v1.0 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
NF1 c.3479G>A

NM_001042492.2:c.3479G>A (p.Gly1160Asp) in NF1 is a missense variant absent from gnomAD population databases (v2.1, v4.1, Canada v1.0), satisfying PM2 at supporting strength.1 This variant does not meet PVS1 criteria, as it is a missense variant and does not fall into the null-variant buckets (nonsense, frameshift, canonical splice) defined by the ClinGen SVI PVS1 recommendations (PMC6185798).2 No variant-specific functional studies (PS3/BS3), segregation data (PP1/BS4), de novo observations (PS2/PM6), case-control prevalence (PS4), or same-residue pathogenic comparators (PM5/PS1) were identified in ClinVar or the literature.3 In silico predictions are conflicting: REVEL (0.851) supports a deleterious effect while BayesDel (0.15882) is in the benign range, and SpliceAI predicts no splice impact (max delta 0.06). These conflicting results preclude application of both PP3 and BP4.4 ClinVar classification is Likely pathogenic with review status 'criteria provided, single submitter' (2★); conflicting submissions exist (2 LP, 2 VUS, 1 P). PP5 does not apply at this review level and BP6 is not met as no benign classification exists.5 The NF1 CSPEC framework (ClinGen Neurofibromatosis and Schwannomatosis Expert Panel, Version 1.0) was retrieved but is incomplete (framework_complete=false, empty criteria). Generic ACMG/AMP 2015 combination rules (PMID:25741868) are applied for final classification.6 With only one supporting pathogenic criterion (PM2) met and no benign criteria, this variant does not reach the threshold for Likely Pathogenic or Likely Benign classification under generic ACMG/AMP 2015 rules. The variant is classified as a Variant of Uncertain Significance (VUS).7

PM2 VUS
2 pvs1_generic_framework ↗pvs1_variant_assessment
3 clinvar ↗pm5_candidates
4 revelbayesdelspliceai ↗
6 final_classification_frameworkgeneric_acmg_combination_rules
7 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 · 1 applied · 22 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases, consistent with a rare variant. Under generic ACMG/AMP 2015, absence from large population cohorts supports PM2 at supporting strength.
Absent from gnomAD v2.1 (exomes)absent from gnomAD v4.1 (exomes)absent from gnomAD-Canada v1.0 (genomes).
Assessed · not applied
Pathogenic
PS1 No evidence of a different nucleotide change at the same codon resulting in the same amino acid substitution that has been established as pathogenic.
PS2 No de novo observation confirmed for NM_001042492.2:c.3479G>A.
PS3 No variant-specific functional data identified for p.Gly1160Asp.
PS4 No case-control prevalence data available.
PM1 This variant (p.Gly1160Asp) is not located in a statistically significant mutational hotspot per cancerhotspots.org.
PM5 No confirmed pathogenic variant at the same amino acid position (Gly1160) with a different amino acid change was identified.
PM6 No de novo observation with unconfirmed maternity/paternity reported for this variant.
PP1 No segregation data available for this variant.
PP2 Insufficient data to determine if NF1 has a low rate of benign missense variation.
PP3 In silico predictions are conflicting.
PP4 No patient phenotype or family history data available to assess whether the clinical presentation is highly specific for NF1 (neurofibromatosis type 1).
PP5 ClinVar review status for this variant is 'criteria provided, single submitter' (2★).
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 BS1 requires allele frequency greater than expected for the disorder (>0.3% non-VCEP).
BS2 No evidence that this variant has been observed in a healthy adult individual in trans with a known pathogenic dominant variant.
BS3 No well-established functional studies demonstrate no deleterious effect of this variant.
BS4 No family segregation data available.
BP1 NF1 is not a gene where only truncating variants cause disease; missense variants are a well-established pathogenic mechanism in NF1.
BP2 No evidence that this variant is observed in trans with a known pathogenic variant for a fully penetrant dominant disorder.
BP4 Multiple lines of computational evidence do NOT uniformly suggest no impact.
BP5 No evidence that this variant is found in a case with an established alternative molecular basis for disease.
BP6 ClinVar does not classify this variant as benign or likely benign.
N/A · 5 PVS1 · PM3 · PM4 · 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 has been reported in ClinVar as Likely pathogenic (2 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Pathogenic (1 clinical laboratory). (ClinVarID = 861799)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06). REVEL score = 0.851. BayesDel score = 0.15882.
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; COSV104662397, 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 · 8 PMIDs not cited in assessment
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
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
37751797 ↗ Reassessment of the NF1 variants of unknown significance found during the 20-year activity of a genetics diagnostic laboratory. CLINVAR
17636453 ↗ Neurofibromatosis type 1 in genetic counseling practice: recommendations of the National Society of Genetic Counselors. CLINVAR
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
26324357 ↗ American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. CLINVAR
24893135 ↗ Pheochromocytoma and paraganglioma: an endocrine society clinical practice guideline. CLINVAR
33939658 ↗ The North American Neuroendocrine Tumor Society Consensus Guidelines for Surveillance and Management of Metastatic and/or Unresectable Pheochromocytoma and Paraganglioma. CLINVAR