Starting
Initialising…
0%
NF1
Final classification
Likely Benign
NF1 c.4661+11A>G · p.?
NF1

NM_000267.3:c.4661+11A>G is an intronic variant in NF1 (intron 34, +11 position) that has been observed in population databases at low frequency (gnomAD v2.1: 22/282,462 alleles, AF=0.0078%; v4.1: 281/1,612,590 alleles, AF=0.0174%).

Gene
NF1
Transcript
NM_000267.3
HGVS · transcript:coding
NM_000267.3:c.4661+11A>G
Consequence
N/A
GRCh38
chr17:31261868 A>G
GRCh37
chr17:29588886 A>G
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: BS3 supporting benign, BP4 supporting benign, BP6 supporting benign; combination = 3 supporting benign, which maps to Likely Benign.
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: BS3 supporting benign, BP4 supporting benign, BP6 supporting benign; combination = 3 supporting benign, which maps to Likely Benign.
Classification rationale
BS3BP4BP6 Likely Benign
NF1 c.4661+11A>G

NM_000267.3:c.4661+11A>G is an intronic variant in NF1 (intron 34, +11 position) that has been observed in population databases at low frequency (gnomAD v2.1: 22/282,462 alleles, AF=0.0078%; v4.1: 281/1,612,590 alleles, AF=0.0174%).1 Computational splicing prediction (SpliceAI, max delta = 0.10) indicates no significant impact on mRNA splicing.2 A minigene splicing assay (Wimmer et al. 2007, PMID:17295913) demonstrated normal splicing of this variant with no exon skipping or cryptic splice site activation, providing functional evidence against a deleterious splicing effect (BS3_Supporting). Multiple clinical laboratories in ClinVar classify this variant as Likely benign (4 of 7 usable submissions), with no pathogenic classifications reported (BP6_Supporting).3 No pathogenic criteria are met. PVS1 is not applicable as this non-canonical intronic variant does not produce a null allele. PM2 is not met as the variant is present above absence thresholds. PS4 is not met due to population frequency inconsistent with a rare fully penetrant disorder. PS3 is not met as the only functional study shows normal splicing.4 Based on the available evidence (BS3_Supporting, BP4_Supporting, BP6_Supporting), this variant meets criteria for Likely benign classification. Note: BS3 is from a single minigene assay requiring verification; BP4 is from SpliceAI computational prediction; BP6 is from ClinVar clinical laboratory consensus without expert panel review.5

BS3 + BP4 + BP6 Likely Benign
Gene diagram · NM_000267.3 · variants mapped to exon structure
NF1 NM_000267.3
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · supports benign
      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= 0.000174254; MAF= 0.01743%, 281/1612590 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000227155; MAF= 0.02272%, 268/1179810 alleles, homozygotes = 0); grpmax FAF= 0.00020451.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.78866e-05; MAF= 0.00779%, 22/282462 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00015514; MAF= 0.01551%, 20/128916 alleles, homozygotes = 0); grpmax FAF= 0.00010881.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.017% · 281 / 1,612,590
      0 hom · FAF 0.02%
      European (non-Finnish)
      268 / 1,179,810
      0.023%
      Remaining individuals
      6 / 62,356
      0.0096%
      African/African American
      6 / 74,876
      0.008%
      European (Finnish)
      1 / 64,024
      0.0016%
      + 6 not observed (Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0078% · 22 / 282,462
      0 hom · FAF 0.011%
      European (non-Finnish)
      20 / 128,916
      0.016%
      Remaining individuals
      1 / 7,204
      0.014%
      African/African American
      1 / 24,962
      0.004%
      + 5 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      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 = 0.10).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 12 further PMIDs triaged but not cited — see Sources & References.
      PMID 17295913
      Found
      2007 PMID:17295913) No aberrant splicing or cryptic splice site activation detected
      Applied to
      BS3 supports · met
      Sources & reference links
      7Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 12 PMIDs not cited in assessment
      24033266 ↗ A systematic approach to assessing the clinical significance of genetic variants. CLINVAR
      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
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      17636453 ↗ Neurofibromatosis type 1 in genetic counseling practice: recommendations of the National Society of Genetic Counselors. CLINVAR
      20065170 ↗ American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. CLINVAR
      20301288 ↗ Neurofibromatosis 1. CLINVAR
      20301471 ↗ Wilms Tumor Predisposition. CLINVAR
      20664475 ↗ The North American Neuroendocrine Tumor Society consensus guideline for the diagnosis and management of neuroendocrine tumors: pheochromocytoma, paraganglioma, and medullary thyroid cancer. CLINVAR
      24893135 ↗ Pheochromocytoma and paraganglioma: an endocrine society clinical practice guideline. CLINVAR
      26140447 ↗ Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
      33939658 ↗ The North American Neuroendocrine Tumor Society Consensus Guidelines for Surveillance and Management of Metastatic and/or Unresectable Pheochromocytoma and Paraganglioma. CLINVAR