Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
FANCD2
Final classification
VUS
FANCD2 c.70A>G · p.Arg24Gly
FANCD2

NM_033084.4:c.70A>G (p.Arg24Gly) is a missense variant in exon 3 of FANCD2.

Gene
FANCD2
Transcript
NM_033084.4
HGVS · transcript:coding
NM_033084.4:c.70A>G
Consequence
N/A
GRCh38
chr3:10032837 A>G
GRCh37
chr3:10074521 A>G
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
FANCD2 c.70A>G

NM_033084.4:c.70A>G (p.Arg24Gly) is a missense variant in exon 3 of FANCD2. The variant is extremely rare in population databases (gnomAD v4.1 AF 3.1e-06, 5/1,612,676 alleles, 0 homozygotes; absent from gnomAD v2.1 and gnomAD-Canada), meeting PM2 at supporting level.1 Multiple lines of computational evidence (REVEL 0.023, BayesDel -0.631, SpliceAI max delta 0.08) are concordant for a benign interpretation, meeting BP4 at supporting benign level.2 The variant has been reported in ClinVar (VariationID 1692057) by a single submitter (Sema4) as uncertain significance; no reputable source has classified it as pathogenic or benign.3 No functional studies, segregation data, de novo observations, case-control data, or variant-specific literature evidence were identified for this variant.4 Five ClinVar-associated PMIDs were reviewed; none contained variant-specific evidence for NM_033084.4:c.70A>G.5 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) in conflict, and no additional criteria met, the variant is classified as Uncertain Significance (VUS) per generic ACMG/AMP 2015 combination rules.6

PM2 + BP4 VUS
Gene diagram · NM_033084.4 · variants mapped to exon structure
FANCD2 NM_033084.4
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= 3.10044e-06; MAF= 0.00031%, 5/1612676 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.23972e-06; MAF= 0.00042%, 5/1179324 alleles, homozygotes = 0); grpmax FAF= 1.24e-06.
      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
      0.00031% · 5 / 1,612,676
      0 hom · FAF 0.00012%
      European (non-Finnish)
      5 / 1,179,324
      0.00042%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 but submission details could not be extracted. (ClinVarID = 1692057)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.023. BayesDel score = -0.631389.
      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. FANCD2, a tumor suppressor and DNA repair protein, is infrequently altered in cancer. Germline mutations of FANCD2 are associated with the cancer pred
      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 · 5 PMIDs not cited in assessment
      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