16-3729593-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004380.3(CREBBP):c.5454G>A(p.Val1818Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00943 in 1,614,204 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004380.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CREBBP | NM_004380.3 | c.5454G>A | p.Val1818Val | synonymous_variant | Exon 31 of 31 | ENST00000262367.10 | NP_004371.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CREBBP | ENST00000262367.10 | c.5454G>A | p.Val1818Val | synonymous_variant | Exon 31 of 31 | 1 | NM_004380.3 | ENSP00000262367.5 | ||
CREBBP | ENST00000382070.7 | c.5340G>A | p.Val1780Val | synonymous_variant | Exon 30 of 30 | 1 | ENSP00000371502.3 |
Frequencies
GnomAD3 genomes AF: 0.00752 AC: 1145AN: 152226Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00688 AC: 1726AN: 250890Hom.: 15 AF XY: 0.00665 AC XY: 902AN XY: 135658
GnomAD4 exome AF: 0.00963 AC: 14083AN: 1461860Hom.: 99 Cov.: 35 AF XY: 0.00938 AC XY: 6823AN XY: 727236
GnomAD4 genome AF: 0.00752 AC: 1145AN: 152344Hom.: 6 Cov.: 32 AF XY: 0.00741 AC XY: 552AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:3
CREBBP: BP4, BP7, BS1, BS2 -
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not specified Benign:2
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Rubinstein-Taybi syndrome Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at