chr22-41177921-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001429.4(EP300):c.6210G>A(p.Val2070Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000229 in 1,614,154 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001429.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.6210G>A | p.Val2070Val | synonymous_variant | Exon 31 of 31 | 1 | NM_001429.4 | ENSP00000263253.7 | ||
EP300 | ENST00000674155.1 | c.6132G>A | p.Val2044Val | synonymous_variant | Exon 30 of 30 | ENSP00000501078.1 | ||||
ENSG00000232754 | ENST00000415054.1 | n.82+5142C>T | intron_variant | Intron 1 of 2 | 3 | |||||
EP300-AS1 | ENST00000420537.1 | n.224-3097C>T | intron_variant | Intron 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00130 AC: 198AN: 152142Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251414Hom.: 0 AF XY: 0.000294 AC XY: 40AN XY: 135882
GnomAD4 exome AF: 0.000118 AC: 172AN: 1461894Hom.: 1 Cov.: 31 AF XY: 0.000100 AC XY: 73AN XY: 727248
GnomAD4 genome AF: 0.00130 AC: 198AN: 152260Hom.: 2 Cov.: 32 AF XY: 0.00116 AC XY: 86AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:3
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EP300: BP4, BS1, BS2 -
Rubinstein-Taybi syndrome due to EP300 haploinsufficiency Benign:1
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EP300-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at