Variant chr16-3727692-A-AG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004380.3(CREBBP):c.*25_*26insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 1,612,360 control chromosomes in the GnomAD database, including 290 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0083 ( 23 hom., cov: 31)

Exomes 𝑓: 0.012 ( 267 hom. )

Consequence

CREBBP
NM_004380.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.51

Variant links:

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]

CREBBP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 16-3727692-A-AG is Benign according to our data. Variant chr16-3727692-A-AG is described in ClinVar as [Benign]. Clinvar id is 1268812.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CREBBP	NM_004380.3 linkuse as main transcript	c.25_26insC		3_prime_UTR_variant	31/31	ENST00000262367.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CREBBP	ENST00000262367.10 linkuse as main transcript	c.25_26insC		3_prime_UTR_variant	31/31	1	NM_004380.3	P1	Q92793-1
CREBBP	ENST00000382070.7 linkuse as main transcript	c.25_26insC		3_prime_UTR_variant	30/30	1			Q92793-2

Frequencies

GnomAD3 genomes

AF:

0.00827

AC:

1244

AN:

150498

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00178

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00843

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.0148

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00728

Gnomad OTH

AF:

0.0130

GnomAD3 exomes

AF:

0.0147

AC:

3686

AN:

250384

Hom.:

AF XY:

0.0172

AC XY:

2327

AN XY:

135570

show subpopulations

Gnomad AFR exome

AF:

0.00162

Gnomad AMR exome

AF:

0.00504

Gnomad ASJ exome

AF:

0.0471

Gnomad EAS exome

AF:

0.0191

Gnomad SAS exome

AF:

0.0524

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.00833

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.0119

AC:

17397

AN:

1461748

Hom.:

267

Cov.:

AF XY:

0.0133

AC XY:

9694

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.00188

Gnomad4 AMR exome

AF:

0.00541

Gnomad4 ASJ exome

AF:

0.0466

Gnomad4 EAS exome

AF:

0.0235

Gnomad4 SAS exome

AF:

0.0521

Gnomad4 FIN exome

AF:

0.00186

Gnomad4 NFE exome

AF:

0.00831

Gnomad4 OTH exome

AF:

0.0153

GnomAD4 genome

AF:

0.00826

AC:

1244

AN:

150612

Hom.:

Cov.:

AF XY:

0.00879

AC XY:

648

AN XY:

73690

show subpopulations

Gnomad4 AFR

AF:

0.00177

Gnomad4 AMR

AF:

0.00842

Gnomad4 ASJ

AF:

0.0476

Gnomad4 EAS

AF:

0.0147

Gnomad4 SAS

AF:

0.0549

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00728

Gnomad4 OTH

AF:

0.0129

Alfa

AF:

0.0119

Hom.:

Bravo

AF:

0.00755

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over