rs1555742114
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_004364.5(CEBPA):c.569C>T(p.Ser190Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000381 in 1,313,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S190P) has been classified as Uncertain significance.
Frequency
Consequence
NM_004364.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEBPA | NM_004364.5 | c.569C>T | p.Ser190Leu | missense_variant | 1/1 | ENST00000498907.3 | |
CEBPA | NM_001287424.2 | c.674C>T | p.Ser225Leu | missense_variant | 1/1 | ||
CEBPA | NM_001287435.2 | c.527C>T | p.Ser176Leu | missense_variant | 1/1 | ||
CEBPA | NM_001285829.2 | c.212C>T | p.Ser71Leu | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEBPA | ENST00000498907.3 | c.569C>T | p.Ser190Leu | missense_variant | 1/1 | NM_004364.5 | P1 | ||
ENST00000587312.1 | n.388G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000675 AC: 1AN: 148072Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000343 AC: 4AN: 1165692Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 569922
GnomAD4 genome ? AF: 0.00000675 AC: 1AN: 148072Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72066
ClinVar
Submissions by phenotype
Acute myeloid leukemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 25, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 526806). This variant has not been reported in the literature in individuals affected with CEBPA-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 190 of the CEBPA protein (p.Ser190Leu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at