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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 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1 and present at an extremely low allele frequency in gnomAD v4.1 (AF = 3.11e-6; 5/1,608,878 alleles; no homozygotes). This is well below the 0.1% PM2 threshold for dominant disorders under generic ACMG/AMP rules. The variant is also absent from ClinVar and gnomAD-Canada.
gnomAD v2.1: absent. gnomAD v4.1: AF = 3.11e-6 (5/1608878)
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on gene or gene product. SpliceAI predicts no splice alteration (max delta = 0.00). REVEL score is 0.388, below the typical pathogenic cutoff. BayesDel score is -0.135549, in the benign/neutral range. No in silico predictor supports a deleterious effect.
SpliceAI: max delta = 0.00 (all delta scores = 0.00). REVEL: 0.388 (below pathogenic threshold of ~0.5-0.75). BayesDel: -0.135549 (negativeconsistent with benign).
Assessed · not applied
Pathogenic
PS1 PS1 requires a different nucleotide change at the same codon producing the same amino acid change previously established as pathogenic.
PS2 PS2 requires a confirmed de novo observation (maternity and paternity confirmed) in a patient with CREBBP-associated disease.
PS3 PS3 requires well-established in vitro or in vivo functional studies supportive of a damaging effect.
PS4 PS4 requires statistically significant enrichment of the variant in affected individuals versus controls.
PM1 PM1 requires location in a mutational hot spot or well-established critical functional domain without benign variation.
PM6 PM6 requires a de novo observation without confirmation of both parents.
PP1 PP1 requires co-segregation of the variant with disease in multiple affected family members.
PP2 PP2 applies to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism.
PP3 PP3 requires multiple lines of computational evidence supporting a deleterious effect.
PP4 PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5 PP5 requires a reputable source to have reported this variant as pathogenic with supporting evidence.
Benign
BA1 BA1 requires an allele frequency >1% in any general population database.
BS1 BS1 requires an allele frequency >0.3% for a dominant disorder.
BS2 BS2 requires observation in a healthy adult individual for a fully penetrant dominant disorder.
BS3 BS3 requires well-established functional studies showing no damaging effect.
BS4 BS4 requires non-segregation with disease in affected members of a family.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease.
BP2 BP2 requires observation in trans with a known pathogenic variant for a fully penetrant dominant disorder.
BP5 BP5 requires observation of the variant in a case with an alternative molecular basis for disease.
BP6 BP6 requires a reputable source to report the variant as benign without the evaluator independently reviewing the evidence.
BP7 BP7 applies to synonymous variants predicted to have no splice impact.
N/A · 2 PVS1 · PM5
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= 3.10776e-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.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031% · 5 / 1,608,878
0 hom · FAF 7.9e-05%
African/African American
1 / 74,808
0.0013%
European (non-Finnish)
4 / 1,179,576
0.00034%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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