rs1046088
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001429.4(EP300):āc.6668A>Cā(p.Gln2223Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 1,614,146 control chromosomes in the GnomAD database, including 883 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 Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q2223K) 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 -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EP300 | NM_001429.4 | c.6668A>C | p.Gln2223Pro | missense_variant | 31/31 | ENST00000263253.9 | |
EP300 | NM_001362843.2 | c.6590A>C | p.Gln2197Pro | missense_variant | 30/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.6668A>C | p.Gln2223Pro | missense_variant | 31/31 | 1 | NM_001429.4 | P2 | |
ENST00000415054.1 | n.82+4684T>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
EP300-AS1 | ENST00000420537.1 | n.224-3555T>G | intron_variant, non_coding_transcript_variant | 3 | |||||
EP300 | ENST00000674155.1 | c.6590A>C | p.Gln2197Pro | missense_variant | 30/30 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0234 AC: 3563AN: 152154Hom.: 59 Cov.: 32
GnomAD3 exomes AF: 0.0238 AC: 5967AN: 251224Hom.: 91 AF XY: 0.0235 AC XY: 3185AN XY: 135790
GnomAD4 exome AF: 0.0311 AC: 45443AN: 1461874Hom.: 824 Cov.: 32 AF XY: 0.0303 AC XY: 22043AN XY: 727236
GnomAD4 genome ? AF: 0.0234 AC: 3563AN: 152272Hom.: 59 Cov.: 32 AF XY: 0.0228 AC XY: 1701AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:2Other:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 07, 2013 | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Rubinstein-Taybi syndrome due to EP300 haploinsufficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 11, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at