Starting
Initialising…
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CREBBP
Final classification
VUS
CREBBP c.5671G>A · p.Gly1891Arg
CREBBP

CREBBP NM_004380.2:c.5671G>A (p.Gly1891Arg) is a missense variant in exon 31 of CREBBP, a gene associated with autosomal dominant Rubinstein-Taybi syndrome through haploinsufficiency and loss-of-function mechanisms.

Gene
CREBBP
Transcript
NM_004380.2
HGVS · transcript:coding
NM_004380.2:c.5671G>A
Consequence
N/A
GRCh38
chr16:3729376 C>T
GRCh37
chr16:3779377 C>T
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
CREBBP c.5671G>A

CREBBP NM_004380.2:c.5671G>A (p.Gly1891Arg) is a missense variant in exon 31 of CREBBP, a gene associated with autosomal dominant Rubinstein-Taybi syndrome through haploinsufficiency and loss-of-function mechanisms.1 The variant is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (allele frequency 3.11e-6; 5/1,608,878 alleles; no homozygotes), meeting PM2 at supporting strength for a dominant disorder.2 Multiple in silico tools do not support a deleterious effect: SpliceAI predicts no splice alteration (max delta = 0.00), REVEL score is 0.388 (below typical pathogenic threshold), and BayesDel score is -0.135549 (benign range), meeting BP4 at supporting benign strength.3 The variant is absent from ClinVar, and no published literature specifically reporting NM_004380.2:c.5671G>A was identified across five screened abstracts addressing CREBBP in germline disease contexts.4 No functional studies, de novo observations, co-segregation data, or case-control evidence was identified for this variant. PVS1 is not applicable as the variant is missense, not a null variant.5 Under generic ACMG/AMP 2015 combination rules, the applicable criteria are PM2 (supporting) and BP4 (supporting benign). These partially offset, resulting in an overall classification of Variant of Uncertain Significance (VUS).6 The observation of five carriers in gnomAD v4.1 (including one in the African/African American subpopulation) without homozygotes is noted; however, in the absence of individual-level phenotype data, this does not independently establish benignity. The gnomAD filtering allele frequency (grpmax FAF = 7.9e-7) confirms extreme rarity.7

PM2 + BP4 VUS
1 pvs1_gene_context
3 spliceai ↗revelbayesdel
5 pvs1_variant_assessmentoncokb ↗
6 generic_acmg_combination_rules
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
      Overall AF
      5 / 1,608,878
      0.00031%
      Highest · African/African American
      0.0013%
      Homozygotes
      0
      grpmax FAF
      7.9e-05%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 2 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      African/African American 1 / 74,808 0.0013% 0
      European (non-Finnish) 4 / 1,179,576 0.00034% 0
      Admixed American 0 / 59,858
      European (Finnish) 0 / 59,848
      Amish 0 / 910
      East Asian 0 / 44,834
      Middle Eastern 0 / 6,082
      South Asian 0 / 90,990
      Ashkenazi Jewish 0 / 29,566
      This variant is present in gnomAD v4.1 (AF= 3.10776e-06; MAF= 0.00031%, 5/1608878 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33676e-05; MAF= 0.00134%, 1/74808 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      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 no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.388. BayesDel score = -0.135549.
      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. CREBBP, a tumor suppressor and transcriptional co-activator, is frequently inactivated in hematologic malignancies.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots