Starting
Initialising…
0%
FANCD2
Final classification
VUS
FANCD2 c.266A>G · p.Tyr89Cys
FANCD2

PM2 is met at moderate strength: the variant is absent from gnomAD v2.1 and v4.1 population databases.

Gene
FANCD2
Transcript
NM_033084.4
HGVS · transcript:coding
NM_033084.4:c.266A>G
Consequence
N/A
GRCh38
chr3:10034529 A>G
GRCh37
chr3:10076213 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 moderate, BP4 supporting benign; combination = 1 moderate + 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
FANCD2 c.266A>G

PM2 is met at moderate strength: the variant is absent from gnomAD v2.1 and v4.1 population databases.1 BP4 is met at supporting benign strength: REVEL (0.297), BayesDel (-0.03757), and SpliceAI (max delta 0.02) all predict a neutral or non-damaging effect.2 PVS1 is not applicable because this is a missense substitution (p.Tyr89Cys), not a null variant per ClinGen PVS1 recommendations (PMC6185798).3 PP3 is not met: the same in silico evidence that supports BP4 fails to support a pathogenic computational prediction.4 The majority of criteria (PS1-PS4, PM1, PM6, PP1-PP2, PP4, BS2-BS4, BP2, BP5-BP6) cannot be assessed due to a complete absence of variant-specific data in ClinVar, gnomAD, the literature, and functional databases.5 Under the generic ACMG/AMP 2015 combination rules (PMID:25741868), one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) do not meet the threshold for likely pathogenic (requires ≥3 moderate or 1 strong + ≥1 moderate) or likely benign (requires ≥2 supporting benign or 1 strong benign + 1 supporting benign). The variant is classified as a Variant of Uncertain Significance (VUS).6

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
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
      Absent from gnomAD v4.1.
      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
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.297. BayesDel score = -0.03757.
      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