22-41135824-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001429.4(EP300):āc.1540A>Gā(p.Met514Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001429.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152050Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251442Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135894
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1460932Hom.: 0 Cov.: 30 AF XY: 0.0000743 AC XY: 54AN XY: 726854
GnomAD4 genome AF: 0.000105 AC: 16AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74396
ClinVar
Submissions by phenotype
EP300-related disorder Uncertain:1
The EP300 c.1540A>G variant is predicted to result in the amino acid substitution p.Met514Val. To our knowledge, this variant has not been reported in individuals with EP300-related disorders in the literature. This variant is reported in 0.035% of alleles in individuals of East Asian descent in gnomAD, which is likely too common to be a fully penetrant cause of disease. Although we suspect this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
not provided Uncertain:1
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Rubinstein-Taybi syndrome due to EP300 haploinsufficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at