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CREBBP
Final classification
VUS
CREBBP c.3710G>C · p.Cys1237Ser
CREBBP

This variant is absent from population databases (gnomAD v2.1, v4.1, Canada; AF=0%), meeting PM2 at moderate strength.

Gene
CREBBP
Transcript
NM_004380.2
HGVS · transcript:coding
NM_004380.2:c.3710G>C
Consequence
N/A
GRCh38
chr16:3751795 C>G
GRCh37
chr16:3801796 C>G
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 moderate, PP3 supporting; combination = 1 moderate + 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 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
CREBBP c.3710G>C

This variant is absent from population databases (gnomAD v2.1, v4.1, Canada; AF=0%), meeting PM2 at moderate strength.1 Multiple in silico predictors support a deleterious effect: REVEL score 0.922 is strongly pathogenic, and BayesDel additive score 0.549 supports deleteriousness, meeting PP3 at supporting strength.2 No other pathogenic criteria were met. PVS1 is not applicable (missense variant). PS3 was not met (no functional data identified). PS1, PS4, PS5, PM1, PM5, and PP5 did not yield evidence for this variant.3 No benign criteria were met. BA1 and BS1 are not met (variant absent from population databases). BP1 is not met (missense variants are established in CREBBP disease). BP4 is not met (in silico predictors favor pathogenicity).4 Total evidence: 1 moderate pathogenic criterion (PM2) + 1 supporting pathogenic criterion (PP3). This does not meet the threshold for Likely Pathogenic (requires 2 moderate + 2 supporting, or 1 moderate + 4 supporting, or 1 strong + 2 supporting, etc.) per generic ACMG/AMP 2015 combination rules.5 The variant is classified as a Variant of Uncertain Significance (VUS). The missense substitution p.Cys1237Ser in the PHD finger domain of CREBBP, complete absence from population databases, and concordant in silico predictions warrant further investigation including functional studies, segregation analysis, and clinical correlation.6

PM2 + PP3 VUS
2 revelbayesdel
3 pvs1_variant_assessmentclinvar ↗oncokb ↗pm5_candidates
5 generic_acmg_combination_rules
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 · 19 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases. Allele frequency of 0% is well below the PM2 threshold of <0.1%.
Absent from gnomAD v2.1 (AF=0)gnomAD v4.1 (AF=0)and gnomAD-Canada v1.0 (AF=0).
PP3 supporting Pathogenic
Multiple in silico predictors support a deleterious effect. REVEL score is 0.922, which is well above the pathogenic threshold of 0.5. BayesDel additive score is 0.549, also above the deleterious threshold of 0.27. SpliceAI predicts no significant splice impact (max delta 0.13), which is expected for a missense variant.
REVEL score: 0.922 (pathogenic). BayesDel additive score: 0.549 (deleterious). SpliceAI max delta: 0.13 (no splicing impact).
Assessed · not applied
Pathogenic
PS1 No evidence of a different nucleotide change at the same codon resulting in the same amino acid substitution (p.Cys1237Ser) that is established as pathogenic.
PS2 No de novo data available in the case materials.
PS3 No functional studies were identified for this variant.
PS4 No prevalence data available.
PM1 Position 1237 lies within the PHD finger zinc-binding domain of CREBBP, which is a recognized functional domain.
PM5 No pathogenic missense variants at the same amino acid residue (Cys1237) were identified in ClinVar.
PM6 No de novo data available.
PP1 No segregation data available.
PP2 The HCI prior missense constraint score is not available for CREBBP.
PP4 No patient phenotype data was provided.
Benign
BA1 The variant is absent from gnomAD (AF=0%), far below the BA1 threshold of >1% allele frequency in population databases.
BS1 The variant is absent from gnomAD (AF=0%), far below the BS1 threshold of >0.3% allele frequency.
BS2 No data on observation in healthy adults with complete penetrance expected at an early age.
BS3 No functional studies demonstrating no damaging effect were identified.
BS4 No segregation data available.
BP1 CREBBP missense variants are established causes of Rubinstein-Taybi syndrome.
BP2 No data on observation in trans with a known pathogenic variant.
BP4 Multiple in silico predictors support a deleterious effect, not a benign impact.
BP5 No alternative molecular diagnosis data available.
N/A · 7 PVS1 · PM3 · PM4 · PP5 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 = 0.13). REVEL score = 0.922. BayesDel score = 0.549047.
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 previously been reported in somatic cancers (COSMIC; COSV108055186, 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