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CTNNB1
Final classification
VUS
CTNNB1 c.643G>A · p.Ala215Thr
CTNNB1

This variant is present at extremely low frequency in population databases (gnomAD v2.1: 4/282,282 alleles, AF=0.0014%; gnomAD v4.1: 62/1,613,818 alleles, AF=0.0038%; absent from gnomAD-Canada), meeting PM2 at supporting strength.

Gene
CTNNB1
Transcript
NM_001904.4
HGVS · transcript:coding
NM_001904.4:c.643G>A
Consequence
N/A
GRCh38
chr3:41225481 G>A
GRCh37
chr3:41266972 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; combination = 1 supporting, 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
CTNNB1 c.643G>A

This variant is present at extremely low frequency in population databases (gnomAD v2.1: 4/282,282 alleles, AF=0.0014%; gnomAD v4.1: 62/1,613,818 alleles, AF=0.0038%; absent from gnomAD-Canada), meeting PM2 at supporting strength.1 In silico predictors do not support a deleterious effect: REVEL score is 0.278, BayesDel is 0.13681, and SpliceAI predicts no splicing impact (max delta 0.02). However, these scores are insufficient to independently meet BP4.2 This variant has been reported in ClinVar as Likely benign by one clinical laboratory (GeneDx) and as Uncertain significance by another (Labcorp/Invitae). No pathogenic classification has been asserted by any submitter.3 No functional studies, segregation data, de novo observations, or variant-specific publications were identified for this variant. OncoKB reports Unknown Oncogenic Effect with no curated functional evidence.4 With only one supporting-level pathogenic criterion (PM2) met and no benign criteria met, the evidence is insufficient to classify this variant as either pathogenic or benign. This variant is classified as a Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 rules (PMID:25741868).5

PM2 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_001904.4 · variants mapped to exon structure
CTNNB1 NM_001904.4
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 3.84182e-05; MAF= 0.00384%, 62/1613818 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 4.80215e-05; MAF= 0.00480%, 3/62472 alleles, homozygotes = 0); grpmax FAF= 3.666e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.41702e-05; MAF= 0.00142%, 4/282282 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 5.02008e-05; MAF= 0.00502%, 1/19920 alleles, homozygotes = 0); grpmax FAF= 2.93e-06.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0038% · 62 / 1,613,818
      0 hom · FAF 0.0037%
      Remaining individuals
      3 / 62,472
      0.0048%
      European (non-Finnish)
      55 / 1,179,980
      0.0047%
      African/African American
      2 / 74,904
      0.0027%
      East Asian
      1 / 44,886
      0.0022%
      South Asian
      1 / 91,068
      0.0011%
      + 5 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0014% · 4 / 282,282
      0 hom · FAF 0.00029%
      East Asian
      1 / 19,920
      0.005%
      African/African American
      1 / 24,950
      0.004%
      European (non-Finnish)
      2 / 128,882
      0.0016%
      + 5 not observed (Admixed American, Ashkenazi Jewish, 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 Likely benign (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 1200393)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.278. BayesDel score = 0.13681.
      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. CTNNB1 (β-catenin), a transcriptional activator, is recurrently mutated in various cancers including endometrial and hepatocellular 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 previously been reported in somatic cancers (COSMIC; COSV62719230, n = 1 times).
      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