Starting
Initialising…
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CREBBP
Final classification
VUS
CREBBP c.3609+1G>T · p.?
CREBBP

NM_004380.2:c.3609+1G>T is a canonical splice donor (+1) variant in CREBBP. Loss of function in CREBBP is an established mechanism for Rubinstein-Taybi syndrome (PMID:41153422). Under ClinGen SVI PVS1 recommendations (PMC6185798), canonical splice variants in genes with established LOF disease mechanism are assigned PVS1 at very strong strength.

Gene
CREBBP
Transcript
NM_004380.2
HGVS · transcript:coding
NM_004380.2:c.3609+1G>T
Consequence
N/A
GRCh38
chr16:3757808 C>A
GRCh37
chr16:3807809 C>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: PVS1 very strong, PM2 supporting; combination = 1 very strong + 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: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
CREBBP c.3609+1G>T

NM_004380.2:c.3609+1G>T is a canonical splice donor (+1) variant in CREBBP. Loss of function in CREBBP is an established mechanism for Rubinstein-Taybi syndrome (PMID:41153422). Under ClinGen SVI PVS1 recommendations (PMC6185798), canonical splice variants in genes with established LOF disease mechanism are assigned PVS1 at very strong strength.1 The variant is absent from gnomAD v2.1 and v4.1 population databases (0 alleles observed), meeting PM2 at supporting strength under the generic ACMG/AMP <0.1% allele frequency threshold.2 SpliceAI predicts strong disruption of the canonical splice donor (max delta score = 1.00; donor loss = 1.0, donor gain = 0.84). This in silico evidence is consistent with PVS1 but is not separately scored as PP3 per PMC6185798 guidance to avoid double-counting splice prediction evidence.3 No verified clinical observations (de novo status, case counts, co-segregation, or functional data) for this exact variant were identified. ClinVar has no entry. Multiple criteria (PS2, PS3, PS4, PM6, PP1, PP4) could not be assessed due to absence of variant-specific evidence.4 Under the generic ACMG/AMP 2015 final classification rules (PMID:25741868), PVS1 (very strong) with PM2 (supporting) does not meet the threshold for Pathogenic (requires ≥2 supporting or 1 moderate + 1 supporting with PVS1) or Likely Pathogenic (requires PVS1 + 1 moderate). The variant is classified as a Variant of Uncertain Significance (VUS). Clinical corroboration through case-level evidence (de novo observation, co-segregation, or functional studies) would be needed to resolve the classification.5

PVS1 + PM2 VUS
Gene diagram · NM_004380.2 · variants mapped to exon structure
CREBBP NM_004380.2
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
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 1.00). BayesDel score = 0.66.
      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 not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      6Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC