22-41093033-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PP3_ModerateBP6BS2
The ENST00000263253.9(EP300):āc.29C>Gā(p.Pro10Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,614,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P10S) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000263253.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EP300 | NM_001429.4 | c.29C>G | p.Pro10Arg | missense_variant | 1/31 | ENST00000263253.9 | NP_001420.2 | |
EP300 | NM_001362843.2 | c.29C>G | p.Pro10Arg | missense_variant | 1/30 | NP_001349772.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.29C>G | p.Pro10Arg | missense_variant | 1/31 | 1 | NM_001429.4 | ENSP00000263253 | P2 | |
EP300 | ENST00000674155.1 | c.29C>G | p.Pro10Arg | missense_variant | 1/30 | ENSP00000501078 | A2 | |||
EP300 | ENST00000703544.1 | c.29C>G | p.Pro10Arg | missense_variant, NMD_transcript_variant | 1/30 | ENSP00000515365 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251076Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135834
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727214
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
EP300-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 04, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at