chr19-33301839-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS2
The NM_004364.5(CEBPA):c.576G>T(p.Pro192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,141,810 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P192P) has been classified as Likely benign.
Frequency
Consequence
NM_004364.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEBPA | NM_004364.5 | c.576G>T | p.Pro192= | synonymous_variant | 1/1 | ENST00000498907.3 | |
CEBPA | NM_001287424.2 | c.681G>T | p.Pro227= | synonymous_variant | 1/1 | ||
CEBPA | NM_001287435.2 | c.534G>T | p.Pro178= | synonymous_variant | 1/1 | ||
CEBPA | NM_001285829.2 | c.219G>T | p.Pro73= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEBPA | ENST00000498907.3 | c.576G>T | p.Pro192= | synonymous_variant | 1/1 | NM_004364.5 | P1 | ||
ENST00000587312.1 | n.381C>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000438 AC: 5AN: 1141810Hom.: 0 Cov.: 31 AF XY: 0.00000538 AC XY: 3AN XY: 557328
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 04, 2021 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Apr 13, 2021 | - - |
Acute myeloid leukemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at