rs1555912151
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM4PP3BS2
The NM_001429.4(EP300):βc.5556_5564delβ(p.Ala1853_Pro1855del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,886 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (β β ). Synonymous variant affecting the same amino acid position (i.e. P1850P) has been classified as Likely benign.
Frequency
Consequence
NM_001429.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EP300 | NM_001429.4 | c.5556_5564del | p.Ala1853_Pro1855del | inframe_deletion | 31/31 | ENST00000263253.9 | |
EP300 | NM_001362843.2 | c.5478_5486del | p.Ala1827_Pro1829del | inframe_deletion | 30/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EP300 | ENST00000263253.9 | c.5556_5564del | p.Ala1853_Pro1855del | inframe_deletion | 31/31 | 1 | NM_001429.4 | P2 | |
ENST00000415054.1 | n.82+5795_82+5803del | intron_variant, non_coding_transcript_variant | 3 | ||||||
EP300-AS1 | ENST00000420537.1 | n.224-2444_224-2436del | intron_variant, non_coding_transcript_variant | 3 | |||||
EP300 | ENST00000674155.1 | c.5478_5486del | p.Ala1827_Pro1829del | inframe_deletion | 30/30 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461886Hom.: 1 AF XY: 0.00000688 AC XY: 5AN XY: 727242
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2017 | - - |
Rubinstein-Taybi syndrome due to EP300 haploinsufficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 16, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 521831). This variant has not been reported in the literature in individuals affected with EP300-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.5556_5564del, results in the deletion of 3 amino acid(s) of the EP300 protein (p.Ala1853_Pro1855del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at