16-3729114-T-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_004380.3(CREBBP):āc.5933A>Gā(p.Asn1978Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00542 in 1,581,462 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_004380.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CREBBP | NM_004380.3 | c.5933A>G | p.Asn1978Ser | missense_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.5933A>G | p.Asn1978Ser | missense_variant | Exon 31 of 31 | 1 | NM_004380.3 | ENSP00000262367.5 | ||
CREBBP | ENST00000382070.7 | c.5819A>G | p.Asn1940Ser | missense_variant | Exon 30 of 30 | 1 | ENSP00000371502.3 |
Frequencies
GnomAD3 genomes AF: 0.00427 AC: 647AN: 151544Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00505 AC: 1024AN: 202582Hom.: 4 AF XY: 0.00492 AC XY: 546AN XY: 110892
GnomAD4 exome AF: 0.00554 AC: 7925AN: 1429794Hom.: 24 Cov.: 34 AF XY: 0.00545 AC XY: 3870AN XY: 710252
GnomAD4 genome AF: 0.00427 AC: 647AN: 151668Hom.: 3 Cov.: 32 AF XY: 0.00403 AC XY: 299AN XY: 74136
ClinVar
Submissions by phenotype
not specified Benign:4Other:1
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
- -
- -
not provided Benign:3
- -
CREBBP: PM5, PP2, BS2 -
- -
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. -
Rubinstein-Taybi syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at