rs369550568
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_004380.3(CREBBP):c.1514C>T(p.Pro505Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000115 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004380.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREBBP | NM_004380.3 | c.1514C>T | p.Pro505Leu | missense_variant | 6/31 | ENST00000262367.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREBBP | ENST00000262367.10 | c.1514C>T | p.Pro505Leu | missense_variant | 6/31 | 1 | NM_004380.3 | P1 | |
CREBBP | ENST00000382070.7 | c.1400C>T | p.Pro467Leu | missense_variant | 5/30 | 1 | |||
CREBBP | ENST00000570939.2 | c.119C>T | p.Pro40Leu | missense_variant | 1/23 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251468Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135910
GnomAD4 exome AF: 0.000122 AC: 178AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.000109 AC XY: 79AN XY: 727246
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
CREBBP-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 08, 2024 | The CREBBP c.1514C>T variant is predicted to result in the amino acid substitution p.Pro505Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0070% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Rubinstein-Taybi syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2022 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at