Starting
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FANCL
Final classification
VUS
FANCL c.524C>T · p.Ala175Val
FANCL

This variant is absent or extremely rare in large population cohorts: gnomAD v2.1 allele frequency 0.00389% (11/282,764 alleles) and v4.1 allele frequency 0.00229% (37/1,613,586 alleles), meeting PM2 at supporting level.

Gene
FANCL
Transcript
NM_018062.3
HGVS · transcript:coding
NM_018062.3:c.524C>T
Consequence
N/A
GRCh38
chr2:58198610 G>A
GRCh37
chr2:58425745 G>A
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; 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; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
FANCL c.524C>T

This variant is absent or extremely rare in large population cohorts: gnomAD v2.1 allele frequency 0.00389% (11/282,764 alleles) and v4.1 allele frequency 0.00229% (37/1,613,586 alleles), meeting PM2 at supporting level.1 Multiple in silico predictors do not support a deleterious effect: REVEL score 0.089, BayesDel score -0.494, and SpliceAI predicts no splicing impact (max delta 0.04), meeting BP4 at supporting level.2 The variant has been reported in ClinVar as Uncertain significance by 4 clinical laboratories and Likely benign by 1 clinical laboratory (ClinVar Variation ID: 898372). No expert panel classification is available.3 The variant is a missense substitution (p.Ala175Val) and does not qualify for PVS1. No functional studies, segregation data, case-control comparisons, or de novo observations were identified for this variant.4 Applying generic ACMG/AMP 2015 final combination rules (PMID:25741868): PM2_supporting and BP4_supporting provide conflicting lines of evidence with no other criteria met. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 pvs1_variant_assessment
5 generic_acmg_combination_rules
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= 2.29303e-05; MAF= 0.00229%, 37/1613586 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000133329; MAF= 0.01333%, 8/60002 alleles, homozygotes = 0); grpmax FAF= 6.615e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.89017e-05; MAF= 0.00389%, 11/282764 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.96994e-05; MAF= 0.00697%, 9/129126 alleles, homozygotes = 0); grpmax FAF= 3.42e-05.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0023% · 37 / 1,613,586
      0 hom · FAF 0.0066%
      Admixed American
      8 / 60,002
      0.013%
      European (non-Finnish)
      27 / 1,179,588
      0.0023%
      Remaining individuals
      1 / 62,494
      0.0016%
      African/African American
      1 / 75,024
      0.0013%
      + 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0039% · 11 / 282,764
      0 hom · FAF 0.0034%
      European (non-Finnish)
      9 / 129,126
      0.007%
      Admixed American
      2 / 35,424
      0.0056%
      + 6 not observed (African/African American, Ashkenazi Jewish, East Asian, European (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 (4 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 898372)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.089. BayesDel score = -0.494214.
      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 previously been reported in somatic cancers (COSMIC; COSV99288152, n = 1 times).
      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
      25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
      25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. 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
      20301575 ↗ Fanconi Anemia. CLINVAR
      24121147 ↗ Appropriateness of newborn screening for α1-antitrypsin deficiency. CLINVAR
      23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR