rs130025
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004380.3(CREBBP):c.1331-32G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 1,613,734 control chromosomes in the GnomAD database, including 3,179 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.086 ( 1585 hom., cov: 32)
Exomes 𝑓: 0.018 ( 1594 hom. )
Consequence
CREBBP
NM_004380.3 intron
NM_004380.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.332
Genes affected
CREBBP (HGNC:2348): (CREB binding protein) This gene is ubiquitously expressed and is involved in the transcriptional coactivation of many different transcription factors. First isolated as a nuclear protein that binds to cAMP-response element binding protein (CREB), this gene is now known to play critical roles in embryonic development, growth control, and homeostasis by coupling chromatin remodeling to transcription factor recognition. The protein encoded by this gene has intrinsic histone acetyltransferase activity and also acts as a scaffold to stabilize additional protein interactions with the transcription complex. This protein acetylates both histone and non-histone proteins. This protein shares regions of very high sequence similarity with protein p300 in its bromodomain, cysteine-histidine-rich regions, and histone acetyltransferase domain. Mutations in this gene cause Rubinstein-Taybi syndrome (RTS). Chromosomal translocations involving this gene have been associated with acute myeloid leukemia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 16-3782958-C-A is Benign according to our data. Variant chr16-3782958-C-A is described in ClinVar as [Benign]. Clinvar id is 1238727.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREBBP | NM_004380.3 | c.1331-32G>T | intron_variant | ENST00000262367.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREBBP | ENST00000262367.10 | c.1331-32G>T | intron_variant | 1 | NM_004380.3 | P1 | |||
CREBBP | ENST00000382070.7 | c.1217-32G>T | intron_variant | 1 | |||||
CREBBP | ENST00000635753.1 | n.64-32G>T | intron_variant, non_coding_transcript_variant | 5 | |||||
CREBBP | ENST00000636002.1 | n.44-32G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0860 AC: 13061AN: 151934Hom.: 1574 Cov.: 32
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GnomAD3 exomes AF: 0.0316 AC: 7935AN: 250956Hom.: 691 AF XY: 0.0265 AC XY: 3600AN XY: 135688
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GnomAD4 exome AF: 0.0184 AC: 26883AN: 1461682Hom.: 1594 Cov.: 31 AF XY: 0.0175 AC XY: 12758AN XY: 727134
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GnomAD4 genome ? AF: 0.0863 AC: 13119AN: 152052Hom.: 1585 Cov.: 32 AF XY: 0.0819 AC XY: 6086AN XY: 74318
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at