Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
RNF43
Final classification
VUS
RNF43 c.1196C>T · p.Pro399Leu
RNF43

NM_017763.5:c.1196C>T (p.Pro399Leu) is absent from gnomAD v2.1 (0/223,892 alleles) and v4.1 (0/1,595,338 alleles), meeting PM2 at supporting strength.

Gene
RNF43
Transcript
NM_017763.5
HGVS · transcript:coding
NM_017763.5:c.1196C>T
Consequence
N/A
GRCh38
chr17:58358580 G>A
GRCh37
chr17:56435941 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 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
RNF43 c.1196C>T

NM_017763.5:c.1196C>T (p.Pro399Leu) is absent from gnomAD v2.1 (0/223,892 alleles) and v4.1 (0/1,595,338 alleles), meeting PM2 at supporting strength.1 Multiple in silico tools predict a benign effect: REVEL score 0.022, BayesDel score -0.736863, and SpliceAI max delta 0.01 with no predicted splice impact, meeting BP4 at supporting benign strength.2 The variant is reported in ClinVar as Uncertain Significance by a single clinical testing laboratory (VariationID 2093022) with review status 'criteria provided, single submitter.' This does not satisfy PP5 or BP6 thresholds.3 The variant is a missense substitution outside known null-variant buckets, so PVS1 is not applicable. No functional studies, segregation data, de novo observations, case-control evidence, or same-residue pathogenic comparators are available for this variant.4 Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) are present. These are at equal weight and do not meet any pathogenic, likely pathogenic, benign, or likely benign combination threshold.5 Final classification: Uncertain Significance.

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 pvs1_variant_assessmentpm5_candidatesoncokb ↗
5 generic_acmg_combination_rules
Gene diagram · NM_017763.5 · variants mapped to exon structure
RNF43 NM_017763.5
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; MAF= 0.00000%, 0/1595338 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74772 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/223892 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15068 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / 1,595,338
      0 hom
      Not observed in any ancestry group.
      + 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      Absent · 0 / 223,892
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, 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 (1 clinical laboratory). (ClinVarID = 2093022)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.022. BayesDel score = -0.736863.
      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. RNF43, a ubiquitin ligase, is mutated in various cancers including gastrointestinal and gynecological cancers.
      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