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RNF43
Final classification
VUS
PM2BP4
RNF43
c.1196C>T
p.Pro399Leu
This variant

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.

Transcript
NM_017763.5
HGVS · transcript:coding
NM_017763.5:c.1196C>T
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 applied · 18 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_017763.5:c.1196C>T is absent from population databases: gnomAD v2.1 (0/223,892 alleles), gnomAD v4.1 (0/1,595,338 alleles), and gnomAD-Canada v1.0. The observed allele frequency of 0.0% is well below the 0.1% PM2 threshold for rare variants.
gnomAD v2.1: 0/223892 alleles (AF=0.0%)gnomAD v4.1: 0/1
BP4 supporting Benign
Multiple in silico tools consistently predict a benign effect: REVEL score 0.022 (strongly benign-leaning, well below pathogenic threshold), BayesDel score -0.736863 (benign-leaning), and SpliceAI max delta 0.01 (no predicted splicing impact). The convergent benign prediction from independent algorithms supports BP4 at supporting benign strength.
REVEL: 0.022 (benign-leaningtypical pathogenic threshold ~0.5)BayesDel: -0.736863 (benign-leaning)
Assessed · not applied · 16 not met · 2 not assessed
Pathogenic
PS2 No de novo observation of NM_017763.5:c.1196C>T has been reported in the available literature or ClinVar submissions.
PS3 No variant-specific functional studies for NM_017763.5:c.1196C>T (p.Pro399Leu) were identified in the literature or OncoKB.
PS4 No case-control or statistical evidence demonstrates enrichment of NM_017763.5:c.1196C>T in affected individuals compared to controls.
PM1 The variant does not lie in a statistically significant mutational hotspot as determined by cancerhotspots.org, and no known functional domain with established pathogenic missense constraint has been demonstrated to include residue Pro399.
PP1 No segregation data are available for NM_017763.5:c.1196C>T; no co-segregation with disease in affected family members has been reported.
PP2 RNF43 is not established as a gene where missense variants are the predominant pathogenic mechanism with a low rate of benign missense variation.
PP3 Multiple in silico tools predict a benign effect: REVEL score 0.022 (strongly benign-leaning, well below typical pathogenic threshold of ~0.5), BayesDel score -0.736863 (benign-leaning), and SpliceAI max delta 0.01 (no predicted splice impact).
PP4 No phenotype specificity data are available; the variant has not been reported in a cohort where its presence is highly specific to a defined clinical presentation.
PP5 ClinVar reports this variant as Uncertain Significance (VariationID 2093022) from a single clinical testing laboratory (Labcorp Genetics/Invitae) with review status 'criteria provided, single submitter.' This does not constitute a reputable source reporting the variant as pathogenic.
Benign
BA1 NM_017763.5:c.1196C>T is absent from gnomAD (AF=0.0% in both v2.1 and v4.1), far below the 1% BA1 threshold for a benign stand-alone classification.
BS1 NM_017763.5:c.1196C>T is absent from gnomAD (AF=0.0% in both v2.1 and v4.1), far below the 0.3% BS1 threshold for a strong benign criterion.
BS2 No data are available regarding observation of this variant in homozygous state or in healthy adult controls.
BS3 No variant-specific functional studies demonstrating no deleterious effect for NM_017763.5:c.1196C>T (p.Pro399Leu) have been identified.
BS4 No segregation data in unaffected family members are available for this variant.
BP1 RNF43 is not a gene where only truncating variants cause disease.
BP2 No evidence that NM_017763.5:c.1196C>T has been observed in trans with a known pathogenic variant in RNF43.
BP5 No alternative molecular basis for disease has been identified in a case where this variant was observed.
BP6 ClinVar reports NM_017763.5:c.1196C>T as Uncertain Significance (VariationID 2093022) from a single submitter.
N/A · 5 PVS1 · PS1 · PM5 · PM6 · BP7
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