rs552131738
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004364.5(CEBPA):c.789C>T(p.Leu263Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000524 in 1,582,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004364.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEBPA | NM_004364.5 | c.789C>T | p.Leu263Leu | synonymous_variant | Exon 1 of 1 | ENST00000498907.3 | NP_004355.2 | |
CEBPA | NM_001287424.2 | c.894C>T | p.Leu298Leu | synonymous_variant | Exon 1 of 1 | NP_001274353.1 | ||
CEBPA | NM_001287435.2 | c.747C>T | p.Leu249Leu | synonymous_variant | Exon 1 of 1 | NP_001274364.1 | ||
CEBPA | NM_001285829.2 | c.432C>T | p.Leu144Leu | synonymous_variant | Exon 1 of 1 | NP_001272758.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000258 AC: 39AN: 151104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000624 AC: 12AN: 192368Hom.: 0 AF XY: 0.0000658 AC XY: 7AN XY: 106306
GnomAD4 exome AF: 0.0000293 AC: 42AN: 1431304Hom.: 0 Cov.: 31 AF XY: 0.0000267 AC XY: 19AN XY: 710646
GnomAD4 genome AF: 0.000271 AC: 41AN: 151216Hom.: 0 Cov.: 32 AF XY: 0.000271 AC XY: 20AN XY: 73902
ClinVar
Submissions by phenotype
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely 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. -
CEBPA-related disorder Benign:1
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). -
Acute myeloid leukemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at