22-41117723-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001429.4(EP300):c.631G>A(p.Gly211Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0082 in 1,614,214 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G211D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001429.4 missense
Scores
Clinical Significance
Conservation
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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.631G>A | p.Gly211Ser | missense_variant | 2/31 | ENST00000263253.9 | |
EP300 | NM_001362843.2 | c.631G>A | p.Gly211Ser | missense_variant | 2/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.631G>A | p.Gly211Ser | missense_variant | 2/31 | 1 | NM_001429.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00637 AC: 969AN: 152218Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00606 AC: 1524AN: 251410Hom.: 6 AF XY: 0.00592 AC XY: 804AN XY: 135890
GnomAD4 exome AF: 0.00840 AC: 12274AN: 1461878Hom.: 70 Cov.: 32 AF XY: 0.00826 AC XY: 6004AN XY: 727240
GnomAD4 genome ? AF: 0.00635 AC: 968AN: 152336Hom.: 6 Cov.: 33 AF XY: 0.00608 AC XY: 453AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:2Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 01, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | EP300: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 20, 2018 | - - |
EP300-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 19, 2022 | 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 | Feb 01, 2024 | - - |
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
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at