rs147244947

chr22-41117770-C-Gchr22-41117770-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BS1 BS2

The NM_001429.4(EP300):c.678C>G(p.Gly226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,614,220 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0019 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0019 (29 hom.)
• Consequence: EP300 NM_001429.4 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 0.116

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]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 22-41117770-C-G is Benign according to our data. Variant chr22-41117770-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 341781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.116 with no splicing effect.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00194 (296/152344) while in subpopulation EAS AF= 0.0191 (99/5194). AF 95% confidence interval is 0.016. There are 2 homozygotes in gnomad4. There are 167 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd at 294 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EP300	NM_001429.4	c.678C>G	p.Gly226=	synonymous_variant	2/31	ENST00000263253.9
EP300	NM_001362843.2	c.678C>G	p.Gly226=	synonymous_variant	2/30

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EP300	ENST00000263253.9	c.678C>G	p.Gly226=	synonymous_variant	2/31	1	NM_001429.4	P2

Frequencies

GnomAD3 genomes AF: 0.00193 AC: 294 AN: 152226 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00602

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000705

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00258 AC: 648 AN: 251276 Hom.: 3 AF XY: 0.00262 AC XY: 356 AN XY: 135848

Gnomad AFR exome AF: 0.000617

Gnomad AMR exome AF: 0.00310

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0135

Gnomad SAS exome AF: 0.00438

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00110

Gnomad OTH exome AF: 0.00391

GnomAD4 exome AF: 0.00191 AC: 2787 AN: 1461876 Hom.: 29 Cov.: 32 AF XY: 0.00209 AC XY: 1519 AN XY: 727238

Gnomad4 AFR exome AF: 0.000777

Gnomad4 AMR exome AF: 0.00335

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0319

Gnomad4 SAS exome AF: 0.00434

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000722

Gnomad4 OTH exome AF: 0.00214

GnomAD4 genome AF: 0.00194 AC: 296 AN: 152344 Hom.: 2 Cov.: 33 AF XY: 0.00224 AC XY: 167 AN XY: 74512

Gnomad4 AFR AF: 0.000722

Gnomad4 AMR AF: 0.00621

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.00352

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000706

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00167 Hom.: 0

Bravo AF: 0.00235

Asia WGS AF: 0.00779 AC: 27 AN: 3478

EpiCase AF: 0.00125

EpiControl AF: 0.00184

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2023	EP300: BP4, BP7, BS1, BS2 -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 09, 2021	- -

EP300-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 02, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Rubinstein-Taybi syndrome due to EP300 haploinsufficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	9.5
Dann	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8

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

Other links and lift over

dbSNP: rs147244947; hg19: chr22-41513774; COSMIC: COSV54327274; COSMIC: COSV54327274;