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CREBBP
Final classification
Likely Pathogenic
CREBBP c.3780-2A>G · p.?
CREBBP

NM_004380.2:c.3780-2A>G is a canonical splice acceptor variant (position -2 of intron 20) in CREBBP, a gene in which loss of function is an established mechanism for autosomal-dominant Rubinstein-Taybi syndrome.

Gene
CREBBP
Transcript
NM_004380.2
HGVS · transcript:coding
NM_004380.2:c.3780-2A>G
Consequence
N/A
GRCh38
chr16:3749685 T>C
GRCh37
chr16:3799686 T>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: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
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 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
CREBBP c.3780-2A>G

NM_004380.2:c.3780-2A>G is a canonical splice acceptor variant (position -2 of intron 20) in CREBBP, a gene in which loss of function is an established mechanism for autosomal-dominant Rubinstein-Taybi syndrome.1 Under the ClinGen SVI PVS1 decision tree (PMC6185798), this canonical ±1,2 splice variant meets PVS1 at very strong strength given the established CREBBP loss-of-function disease mechanism and absence of downgrade factors.2 The variant is absent from gnomAD v4.1 (0/1,591,234 alleles) and gnomAD v2.1, meeting PM2 at moderate strength.3 SpliceAI strongly predicts an effect on splicing (max delta 1.0, acceptor gain 1.0, acceptor loss 0.99), and BayesDel predicts a deleterious score of 0.66, consistent with a pathogenic splice-altering variant. These in silico predictions are not separately credited under PP3 per PVS1 stacking guidance.4 The variant is absent from ClinVar, and no published case reports, functional studies, or de novo reports were identified for NM_004380.2:c.3780-2A>G in the available literature.5 Overall, the variant meets 1 very strong criterion (PVS1) and 1 moderate criterion (PM2). No benign criteria are met. Per the ACMG/AMP 2015 scoring rubric (1 very strong + 1 moderate), this variant is classified as PATHOGENIC.6

PVS1 + PM2 Likely Pathogenic
1 pvs1_gene_contextpvs1_generic_framework ↗
2 pvs1_generic_framework ↗pvs1_variant_assessment
4 spliceai ↗bayesdel
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 · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
This variant alters the canonical splice acceptor at position -2 of intron 20 in CREBBP (NM_004380.2:c.3780-2A>G). CREBBP loss of function is an established mechanism for Rubinstein-Taybi syndrome, an autosomal-dominant neurodevelopmental disorder. Under the ClinGen SVI PVS1 recommendations (PMC6185798), canonical ±1,2 splice variants in genes with established LoF disease mechanisms are eligible for PVS1 at full strength. The variant is absent from population databases (gnomAD v4.1: 0/1,591,234 alleles), consistent with a pathogenic splice-altering variant under purifying selection. No downgrade factors are present: the affected exon is not absent from biologically relevant transcripts, and population LoF constraint data does not suggest tolerance.
Canonical splice acceptor variant (c.3780-2A>G) at the -2 position of intron 20CREBBP loss of function is an established disease mechanism for Rubinstein-Taybi syndrome (autosomal dominant)Gene eligible for generic PVS1 under PMC6185798
PM2 moderate Pathogenic
This variant is absent from large population databases. In gnomAD v4.1, it is observed at 0/1,591,234 alleles (AF=0.000%), including 0/74656 African/African American alleles. It is also absent from gnomAD v2.1 and gnomAD-Canada v1.0. Under generic ACMG/AMP guidelines, absence from population databases at an allele frequency well below 0.1% meets PM2 at moderate strength.
gnomAD v4.1: 0/1591234 alleles (AF=0.000%)
Assessed · not applied
Pathogenic
PS2 No de novo data are available for this variant.
PS3 No functional data exist for NM_004380.2:c.3780-2A>G or a systematically characterized range that includes this variant.
PS4 This variant is absent from ClinVar and has not been reported in any published case series or cohort studies.
PM1 While CREBBP contains well-characterized functional domains (KIX, bromodomain, HAT/KAT11), the specific region affected by loss of the intron 20 splice acceptor has not been identified as a mutational hotspot or critical functional domain with limited benign variation.
PM6 No de novo occurrence has been documented for this variant.
PP1 No co-segregation data are available for this variant.
PP3 Multiple in silico tools predict a deleterious effect (SpliceAI max delta 1.0, DS_AG=1.0, DS_AL=0.99; BayesDel 0.66).
PP4 No phenotype specificity data are available for this variant.
PP5 This variant is absent from ClinVar.
Benign
BA1 This variant is absent from gnomAD v4.1 (0/1,591,234 alleles, AF=0.000%), far below the BA1 threshold of >1%.
BS1 This variant is absent from gnomAD (AF=0.000%), far below the BS1 threshold of >0.3%.
BS2 BS2 requires observation of the variant in a healthy adult individual with full penetrance expected at an early age.
BS3 No functional studies have assessed NM_004380.2:c.3780-2A>G.
BS4 No lack of segregation data are available.
BP2 No observation of this variant in trans with a known pathogenic CREBBP variant has been reported.
BP4 Multiple lines of computational evidence predict a deleterious effect.
BP5 No data are available demonstrating that this variant has been observed in a case with a definitive alternate molecular basis for disease.
BP6 This variant is absent from ClinVar.
N/A · 5 PS1 · PM5 · PP2 · BP1 · BP7
Research & evidence
Population frequency · supports pathogenic
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= 0; MAF= 0.00000%, 0/1591234 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74656 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
Absent · 0 / 1,591,234
0 hom
Not observed in any ancestry group.
+ 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, 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 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
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC