ClinVar Miner

Submissions for variant NM_001429.4(EP300):c.316A>G (p.Ser106Gly)

gnomAD frequency: 0.00054  dbSNP: rs150245975
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002517583 SCV001091673 likely benign Rubinstein-Taybi syndrome due to EP300 haploinsufficiency 2023-10-20 criteria provided, single submitter clinical testing
GeneDx RCV001355125 SCV001903860 benign not provided 2019-11-13 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001355125 SCV004147974 likely benign not provided 2023-02-01 criteria provided, single submitter clinical testing EP300: BP4, BS1
PreventionGenetics, part of Exact Sciences RCV003935148 SCV004747698 likely benign EP300-related condition 2022-04-14 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
ITMI RCV000120710 SCV000084872 not provided not specified 2013-09-19 no assertion provided reference population
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355125 SCV001549914 likely benign not provided no assertion criteria provided clinical testing The EP300 p.Ser106Gly variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs150245975) and ClinVar (classified as likely benign by Illumina for Rubinstein-Taybi Syndrome). The variant was identified in control databases in 136 of 282856 chromosomes at a frequency of 0.000481 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 129 of 129168 chromosomes (freq: 0.000999), African in 5 of 24964 chromosomes (freq: 0.0002), Other in 1 of 7224 chromosomes (freq: 0.000138) and Latino in 1 of 35440 chromosomes (freq: 0.000028), but was not observed in the Ashkenazi Jewish, East Asian, European (Finnish) or South Asian populations. The p.Ser106 residue is conserved in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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