rs587783466
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 1P and 11B. PP2BP4_ModerateBP6BS1BS2
The NM_004380.3(CREBBP):āc.164A>Gā(p.Asn55Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000424 in 1,461,884 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N55K) has been classified as Uncertain significance.
Frequency
Consequence
NM_004380.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREBBP | NM_004380.3 | c.164A>G | p.Asn55Ser | missense_variant | 2/31 | ENST00000262367.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREBBP | ENST00000262367.10 | c.164A>G | p.Asn55Ser | missense_variant | 2/31 | 1 | NM_004380.3 | P1 | |
CREBBP | ENST00000382070.7 | c.164A>G | p.Asn55Ser | missense_variant | 2/30 | 1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251354Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135898
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461884Hom.: 1 Cov.: 32 AF XY: 0.0000646 AC XY: 47AN XY: 727240
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Rubinstein-Taybi syndrome due to CREBBP mutations;C5193034:Menke-Hennekam syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 03, 2021 | - - |
Rubinstein-Taybi syndrome due to CREBBP mutations Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 19, 2013 | - - |
Rubinstein-Taybi syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at