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FANCL
Final classification
VUS
FANCL c.238C>G · p.Leu80Val
FANCL

NM_018062.3:c.238C>G (p.Leu80Val) in FANCL is a missense variant observed at very low frequency in gnomAD (overall AF 0.015–0.018%) but with two homozygotes in gnomAD v4.1, which is unexpected for a fully penetrant autosomal recessive Fanconi anemia gene.

Gene
FANCL
Transcript
NM_018062.3
HGVS · transcript:coding
NM_018062.3:c.238C>G
Consequence
N/A
GRCh38
chr2:58226763 G>C
GRCh37
chr2:58453898 G>C
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.238C>G

NM_018062.3:c.238C>G (p.Leu80Val) in FANCL is a missense variant observed at very low frequency in gnomAD (overall AF 0.015–0.018%) but with two homozygotes in gnomAD v4.1, which is unexpected for a fully penetrant autosomal recessive Fanconi anemia gene.1 Multiple computational tools predict a benign effect: REVEL score 0.193, BayesDel score -0.271, and SpliceAI max delta 0.04, providing supporting evidence against pathogenicity (BP4_Supporting).2 No functional studies, segregation data, de novo reports, or case-control data are available for this variant. It has been reported in ClinVar as Uncertain significance by six clinical laboratories with no expert panel review.3 No variant-specific evidence was identified in the literature. All ClinVar-associated publications are general guidelines (ACMG/AMP, Sherloc), carrier screening recommendations, GeneReviews, or PDQ cancer genetics summaries that do not mention or evaluate this specific variant.4 Under generic ACMG/AMP 2015 criteria, the available evidence yields one supporting pathogenic criterion (PM2_Supporting) and one supporting benign criterion (BP4_Supporting), resulting in an Uncertain significance classification.5

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= 0.000149416; MAF= 0.01494%, 241/1612942 alleles, homozygotes = 2) and has highest observed frequency in the Middle Eastern population (AF= 0.00165399; MAF= 0.16540%, 10/6046 alleles, homozygotes = 1); grpmax FAF= 0.00089698.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000180677; MAF= 0.01807%, 51/282272 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000818491; MAF= 0.08185%, 25/30544 alleles, homozygotes = 0); grpmax FAF= 0.00056865.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.015% · 241 / 1,612,942
      2 hom · FAF 0.09%
      Middle Eastern
      10 / 6,046
      0.17%
      1 hom
      South Asian
      71 / 90,974
      0.078%
      1 hom
      Remaining individuals
      11 / 62,466
      0.018%
      Admixed American
      9 / 59,944
      0.015%
      European (non-Finnish)
      140 / 1,179,544
      0.012%
      + 5 not observed (European (Finnish), Amish, East Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.018% · 51 / 282,272
      0 hom · FAF 0.057%
      South Asian
      25 / 30,544
      0.082%
      Remaining individuals
      2 / 7,200
      0.028%
      European (non-Finnish)
      20 / 128,888
      0.016%
      Admixed American
      4 / 35,376
      0.011%
      + 4 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish))
      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 (6 clinical laboratories). (ClinVarID = 408230)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.193. BayesDel score = -0.271414.
      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