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FANCL
Final classification
VUS
FANCL c.355G>A · p.Gly119Arg
FANCL

NM_018062.3:c.355G>A (p.Gly119Arg) is a missense variant in exon 5 of FANCL, a gene associated with autosomal recessive Fanconi anemia. PVS1 is not applicable as this is not a null variant.

Gene
FANCL
Transcript
NM_018062.3
HGVS · transcript:coding
NM_018062.3:c.355G>A
Consequence
N/A
GRCh38
chr2:58221961 C>T
GRCh37
chr2:58449096 C>T
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
FANCL c.355G>A

NM_018062.3:c.355G>A (p.Gly119Arg) is a missense variant in exon 5 of FANCL, a gene associated with autosomal recessive Fanconi anemia. PVS1 is not applicable as this is not a null variant.1 This variant is extremely rare in population databases, with an allele frequency of 7.96e-06 (0.0008%) in gnomAD v2.1 and 6.21e-07 (0.00006%) in gnomAD v4.1, meeting PM2 at supporting level.2 Multiple computational predictors (REVEL 0.104, BayesDel -0.400665, SpliceAI max delta 0.03) concordantly suggest a benign effect, meeting BP4 at supporting level.3 The variant has been reported in ClinVar as uncertain significance by two clinical laboratories (ClinVar ID 653483). No pathogenic or benign assertions exist from expert panels.4 Functional data, segregation analysis, de novo observations, case-control studies, and variant-specific literature are all absent for this variant. No publications among the seven reviewed mention NM_018062.3:c.355G>A.5 The balanced evidence profile (PM2_supporting vs. BP4_supporting) results in a net score of zero, consistent with a classification of uncertain significance under ACMG/AMP 2015 generic rules.6

PM2 + BP4 VUS
Gene diagram · NM_018062.3 · variants mapped to exon structure
FANCL NM_018062.3
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= 6.20633e-07; MAF= 0.00006%, 1/1611258 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.23374e-05; MAF= 0.00223%, 1/44768 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.95855e-06; MAF= 0.00080%, 2/251302 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000108731; MAF= 0.01087%, 2/18394 alleles, homozygotes = 0); grpmax FAF= 1.897e-05.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,611,258
      0 hom
      East Asian
      1 / 44,768
      0.0022%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      0.0008% · 2 / 251,302
      0 hom · FAF 0.0019%
      East Asian
      2 / 18,394
      0.011%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      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 (2 clinical laboratories). (ClinVarID = 653483)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.104. BayesDel score = -0.400665.
      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. FANCL, an E3 ubiquitin ligase involved in DNA repair, is infrequently altered in cancer. Germline mutations of FANCL are associated with the cancer pr
      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 not previously been reported in somatic cancers (COSMIC).
      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 · 6 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
      18197057 ↗ Carrier screening in individuals of Ashkenazi Jewish descent. CLINVAR
      20301575 ↗ Fanconi Anemia. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR