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CREBBP
Final classification
VUS
CREBBP c.3215C>G · p.Ser1072Cys
CREBBP

NM_004380.2:c.3215C>G (p.Ser1072Cys) is a missense variant in CREBBP. It is absent from ClinVar and absent from gnomAD v2.1, with a single heterozygous observation in gnomAD v4.1 at extremely low frequency (AF=6.19×10⁻⁷, 1/1,614,258).

Gene
CREBBP
Transcript
NM_004380.2
HGVS · transcript:coding
NM_004380.2:c.3215C>G
Consequence
N/A
GRCh38
chr16:3767755 G>C
GRCh37
chr16:3817756 G>C
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.3215C>G

NM_004380.2:c.3215C>G (p.Ser1072Cys) is a missense variant in CREBBP. It is absent from ClinVar and absent from gnomAD v2.1, with a single heterozygous observation in gnomAD v4.1 at extremely low frequency (AF=6.19×10⁻⁷, 1/1,614,258).1 This low population frequency meets PM2 at supporting strength.2 Multiple computational predictors support a benign impact: REVEL score 0.046 (benign-leaning), BayesDel score -0.448 (predicted benign), and SpliceAI predicts no splice alteration (max Δ=0.00). This meets BP4 at supporting benign strength.3 No variant-specific functional data, de novo observations, segregation data, or published case reports are available. No same-codon pathogenic comparators exist for PM5 or PS1. The variant is not in a mutational hotspot or characterized functional domain.4 The variant does not qualify for PVS1 (missense, not a null variant). BP1 does not apply because missense variants are an established disease mechanism in CREBBP.5 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is balanced and insufficient for classification as pathogenic, likely pathogenic, likely benign, or benign. This variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines.6

PM2 + BP4 VUS
3 revelbayesdelspliceai ↗
4 oncokb ↗clinvar ↗pm5_candidates
5 pvs1_variant_assessment
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
This variant is absent from gnomAD v2.1 (exomes) and present at an extremely low frequency in gnomAD v4.1 (AF=6.19×10⁻⁷, 1/1,614,258 alleles, 0 homozygotes), well below the PM2 threshold of 0.1%.
Absent from gnomAD v2.1single heterozygous observation in gnomAD v4.1 (1/1614
BP4 supporting Benign
Multiple lines of computational evidence support a benign impact: REVEL score 0.046 (well below pathogenic thresholds), BayesDel score -0.448 (predicted benign), and SpliceAI max delta 0.00 (no splice alteration predicted).
REVEL 0.046 (benign-leaningfar below the typical ~0.5 pathogenic threshold)BayesDel -0.448 (negative score
Assessed · not applied
Pathogenic
PS1 No different nucleotide change at codon 1072 has been classified as pathogenic in ClinVar or published literature.
PS2 No de novo observation has been reported for this variant.
PS3 No variant-specific functional data exists.
PS4 No variant prevalence data in affected individuals versus controls.
PM1 Residue 1072 is not in a statistically significant mutational hotspot (cancerhotspots.org: not significant).
PM5 No different pathogenic missense variant at codon 1072 has been identified.
PM6 No de novo observation has been reported for this variant.
PP1 No segregation data is available for this variant.
PP2 While missense variants are a known disease mechanism in CREBBP, PP2 requires demonstrating a low rate of benign missense variation (e.g., via gnomAD missense Z-score or constraint metrics), which was not available in the case evidence.
PP3 Multiple in silico predictors support a benign impact: REVEL score 0.046 (below pathogenic threshold), BayesDel score -0.448 (predicted benign), SpliceAI max delta 0.00 (no splice impact).
PP4 No patient phenotype or family history data is available for this adjudication.
PP5 The variant is absent from ClinVar.
Benign
BA1 The highest population allele frequency is 0.00133% (African/African American, gnomAD v4.1), well below the BA1 threshold of 1%.
BS1 The highest population allele frequency is 0.00133% (African/African American, gnomAD v4.1), well below the BS1 threshold of 0.3% for a dominant disorder.
BS2 A single allele was observed in gnomAD v4.1 (1/1,614,258), but this does not constitute confirmed observation in a healthy adult individual for a fully penetrant dominant disorder.
BS3 No well-established in vitro or in vivo functional studies demonstrate no damaging effect for this variant.
BS4 No segregation data is available for this variant.
BP1 Missense variants are a known disease mechanism in CREBBP.
BP2 No observation of this variant in trans with a pathogenic variant (for a dominant disorder) or in cis with a pathogenic variant (for a recessive disorder) is available.
BP5 No alternative molecular basis for disease has been identified in a case carrying this variant.
BP6 The variant is absent from ClinVar.
N/A · 2 PVS1 · BP7
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= 6.1948e-07; MAF= 0.00006%, 1/1614258 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33216e-05; MAF= 0.00133%, 1/75066 alleles, homozygotes = 0).
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
6.2e-05% · 1 / 1,614,258
0 hom
African/African American
1 / 75,066
0.0013%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish))
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 = 0.046. BayesDel score = -0.448244.
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
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots