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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 applied · 17 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong review Pathogenic
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 germline disease mechanism (serrated polyposis syndrome, colorectal cancer predisposition). Assessed under ClinGen SVI PVS1 recommendations (PMC6185798) as a null variant in a gene with confirmed LOF disease mechanism. SpliceAI predicts no significant splice impact (max delta = 0.0), which conflicts with the canonical splice site expectation; RNA functional studies are recommended to confirm the splicing effect.
Canonical +2 splice donor variant (c.252+2C>G) in intron 2 of RNF43RNF43 loss of function is an established germline disease mechanism (serrated polyposis syndromecolorectal cancer)
PM2 moderate Pathogenic
Extremely rare in population databases. gnomAD v2.1 allele frequency = 3.98e-06 (1/251,184 alleles, 0 homozygotes). gnomAD v4.1 allele frequency = 6.20e-07 (1/1,613,886 alleles, 0 homozygotes). Absent from gnomAD-Canada. Allele frequency is well below the 0.1% PM2 threshold.
gnomAD v2.1 AF = 3.98e-06 (1/251184 alleles0 homozygotes)
Assessed · not applied
Pathogenic
PS2 No de novo observation data available for this variant in any reviewed source.
PS3 No variant-specific functional studies identified.
PS4 No case-control or prevalence data comparing affected individuals to controls available for this variant.
PM6 No de novo observation data available for this variant.
PP1 No cosegregation data available for this variant.
PP3 SpliceAI max delta = 0.0 (no significant splice impact predicted).
PP4 No phenotype specificity data available for affected individuals carrying this variant.
PP5 ClinVar classification is Uncertain significance (2 clinical laboratories, criteria provided, single submitter).
Benign
BA1 gnomAD allele frequency (v2.1: 3.98e-06; v4.1: 6.20e-07) is far below the 1% BA1 threshold.
BS1 gnomAD allele frequency (v2.1: 3.98e-06; v4.1: 6.20e-07) is far below the 0.3% BS1 threshold.
BS2 No data on observation in healthy adults available.
BS3 No variant-specific functional studies demonstrating no deleterious effect were identified.
BS4 No non-segregation data available for this variant.
BP2 No data on observation in trans with a pathogenic variant available.
BP4 SpliceAI predicts no splice impact (max delta = 0.0), but this is insufficient to support a benign interpretation given the canonical splice site position.
BP5 No data on alternate molecular basis for disease in cases carrying this variant.
BP6 ClinVar reports Uncertain significance, not benign or likely benign.
N/A · 9 PS1 · PM1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
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