Variant rs35508493 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000263253.9(EP300):c.*13_*15del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.279 in 1,612,364 control chromosomes in the GnomAD database, including 68,745 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5469 hom., cov: 24)

Exomes 𝑓: 0.28 ( 63276 hom. )

Consequence

EP300
ENST00000263253.9 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 5.78

Variant links:

Genes affected

EP300 (HGNC:3373): (E1A binding protein p300) This gene encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. It functions as histone acetyltransferase that regulates transcription via chromatin remodeling and is important in the processes of cell proliferation and differentiation. It mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. This gene has also been identified as a co-activator of HIF1A (hypoxia-inducible factor 1 alpha), and thus plays a role in the stimulation of hypoxia-induced genes such as VEGF. Defects in this gene are a cause of Rubinstein-Taybi syndrome and may also play a role in epithelial cancer. [provided by RefSeq, Jul 2008]

EP300 links:

(HGNC:):

links:

EP300-AS1 (HGNC:50504): (EP300 antisense RNA 1)

EP300-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 22-41178965-TGTA-T is Benign according to our data. Variant chr22-41178965-TGTA-T is described in ClinVar as [Benign]. Clinvar id is 158555.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-41178965-TGTA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EP300	NM_001429.4 linkuse as main transcript	c.13_15del		3_prime_UTR_variant	31/31	ENST00000263253.9	NP_001420.2
EP300	NM_001362843.2 linkuse as main transcript	c.13_15del		3_prime_UTR_variant	30/30		NP_001349772.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
EP300	ENST00000263253.9 linkuse as main transcript	c.13_15del	3_prime_UTR_variant	31/31	1	NM_001429.4	ENSP00000263253	P2
	ENST00000415054.1 linkuse as main transcript	n.82+4095_82+4097del	intron_variant, non_coding_transcript_variant		3
EP300-AS1	ENST00000420537.1 linkuse as main transcript	n.224-4144_224-4142del	intron_variant, non_coding_transcript_variant		3
EP300	ENST00000674155.1 linkuse as main transcript	c.13_15del	3_prime_UTR_variant	30/30			ENSP00000501078	A2

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37294

AN:

151940

Hom.:

5458

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.428

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.0576

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.267

GnomAD3 exomes

AF:

0.311

AC:

77213

AN:

247962

Hom.:

14938

AF XY:

0.308

AC XY:

41454

AN XY:

134776

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.615

Gnomad ASJ exome

AF:

0.324

Gnomad EAS exome

AF:

0.0617

Gnomad SAS exome

AF:

0.365

Gnomad FIN exome

AF:

0.309

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.327

GnomAD4 exome

AF:

0.282

AC:

412202

AN:

1460306

Hom.:

63276

AF XY:

0.284

AC XY:

206545

AN XY:

726424

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.594

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.0414

Gnomad4 SAS exome

AF:

0.369

Gnomad4 FIN exome

AF:

0.312

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.245

AC:

37316

AN:

152058

Hom.:

5469

Cov.:

AF XY:

0.254

AC XY:

18902

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.0575

Gnomad4 SAS

AF:

0.368

Gnomad4 FIN

AF:

0.312

Gnomad4 NFE

AF:

0.265

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.250

Hom.:

604

Bravo

AF:

0.252

Asia WGS

AF:

0.177

AC:

616

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 10, 2014	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 22, 2018

- -

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