22-41093026-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS2
The ENST00000674155.1(EP300):c.22C>T(p.Pro8Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
ENST00000674155.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.22C>T | p.Pro8Ser | missense_variant | Exon 1 of 31 | 1 | NM_001429.4 | ENSP00000263253.7 | ||
EP300 | ENST00000674155.1 | c.22C>T | p.Pro8Ser | missense_variant | Exon 1 of 30 | ENSP00000501078.1 | ||||
EP300 | ENST00000703544.1 | n.22C>T | non_coding_transcript_exon_variant | Exon 1 of 30 | ENSP00000515365.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461848Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727216 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
EP300-related disorder Uncertain:1
The EP300 c.22C>T variant is predicted to result in the amino acid substitution p.Pro8Ser. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at