Starting
Initialising…
0%
RNF43
Final classification
Likely Pathogenic
RNF43 c.252+2C>G · p.?
RNF43

NM_017763.5:c.252+2C>G is a canonical splice donor variant at the +2 position of intron 2 in RNF43, a gene where loss of function is an established mechanism for germline disease including serrated polyposis syndrome and colorectal cancer predisposition. Assessed under ClinGen SVI PVS1 recommendations (PMC6185798) as a null variant (PVS1).

Gene
RNF43
Transcript
NM_017763.5
HGVS · transcript:coding
NM_017763.5:c.252+2C>G
Consequence
N/A
GRCh38
chr17:58415324 G>C
GRCh37
chr17:56492685 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: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
RNF43 c.252+2C>G

NM_017763.5:c.252+2C>G is a canonical splice donor variant at the +2 position of intron 2 in RNF43, a gene where loss of function is an established mechanism for germline disease including serrated polyposis syndrome and colorectal cancer predisposition. Assessed under ClinGen SVI PVS1 recommendations (PMC6185798) as a null variant (PVS1).1 The variant is extremely rare in population databases, with an allele frequency of 3.98e-06 in gnomAD v2.1 (1/251,184 alleles, 0 homozygotes) and 6.20e-07 in gnomAD v4.1 (1/1,613,886 alleles, 0 homozygotes), and is absent from gnomAD-Canada. Allele frequency is well below the 0.1% PM2 threshold (PM2).2 ClinVar reports this variant as Uncertain significance (2 clinical laboratories, criteria provided, single submitter; Variation ID 3669600). No variant-specific functional studies, segregation data, or de novo observations were identified in the reviewed literature.3 SpliceAI predicts no significant splice impact (max delta = 0.0), which conflicts with the canonical splice site expectation. This discrepancy may reflect SpliceAI calibration for a non-canonical reference donor (C at +2 instead of the consensus T). RNA functional studies are recommended to resolve this conflict.4 Under ACMG/AMP 2015 generic classification rules, 1 Very Strong (PVS1) + 1 Moderate (PM2) supports a classification of Likely Pathogenic. However, the SpliceAI conflict warrants caution and human review.5

PVS1 + PM2 Likely Pathogenic
1 pvs1_gene_contextpvs1_variant_assessmentpvs1_generic_framework ↗
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 · supports pathogenic
      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= 6.19622e-07; MAF= 0.00006%, 1/1613886 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47567e-07; MAF= 0.00008%, 1/1179848 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.98115e-06; MAF= 0.00040%, 1/251184 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80685e-06; MAF= 0.00088%, 1/113548 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,613,886
      0 hom
      European (non-Finnish)
      1 / 1,179,848
      8.5e-05%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0004% · 1 / 251,184
      0 hom
      European (non-Finnish)
      1 / 113,548
      0.00088%
      + 7 not observed (African/African American, Admixed 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 (2 clinical laboratories). (ClinVarID = 3669600)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.65.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has previously been reported in somatic cancers (COSMIC; COSV109424238, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 2 PMIDs not cited in assessment
      17576681 ↗ Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. CLINVAR
      9536098 ↗ Statistical features of human exons and their flanking regions. CLINVAR