rs146242251
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001429.4(EP300):āc.1519A>Gā(p.Ser507Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000781 in 1,614,146 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001429.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EP300 | NM_001429.4 | c.1519A>G | p.Ser507Gly | missense_variant | 6/31 | ENST00000263253.9 | |
EP300 | NM_001362843.2 | c.1519A>G | p.Ser507Gly | missense_variant | 6/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.1519A>G | p.Ser507Gly | missense_variant | 6/31 | 1 | NM_001429.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000894 AC: 136AN: 152178Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00191 AC: 479AN: 250938Hom.: 4 AF XY: 0.00173 AC XY: 235AN XY: 135676
GnomAD4 exome AF: 0.000770 AC: 1125AN: 1461850Hom.: 6 Cov.: 32 AF XY: 0.000745 AC XY: 542AN XY: 727214
GnomAD4 genome ? AF: 0.000893 AC: 136AN: 152296Hom.: 1 Cov.: 31 AF XY: 0.00106 AC XY: 79AN XY: 74478
ClinVar
Submissions by phenotype
Rubinstein-Taybi syndrome due to EP300 haploinsufficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
EP300-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 22, 2023 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 13, 2021 | - - |
Colorectal cancer;C3150941:Rubinstein-Taybi syndrome due to EP300 haploinsufficiency;C4551859:Rubinstein-Taybi syndrome due to CREBBP mutations;C5193035:Menke-Hennekam syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 23, 2021 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at