chr14-23118789-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001805.4(CEBPE):c.303G>A(p.Ala101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000893 in 1,612,792 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 (★). Synonymous variant affecting the same amino acid position (i.e. A101A) has been classified as Likely benign.
Frequency
Consequence
NM_001805.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEBPE | NM_001805.4 | c.303G>A | p.Ala101= | synonymous_variant | 1/2 | ENST00000206513.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEBPE | ENST00000206513.6 | c.303G>A | p.Ala101= | synonymous_variant | 1/2 | 1 | NM_001805.4 | P1 | |
CEBPE | ENST00000696121.1 | n.272G>A | non_coding_transcript_exon_variant | 2/3 | |||||
CEBPE | ENST00000696122.1 | n.49G>A | non_coding_transcript_exon_variant | 2/3 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000844 AC: 21AN: 248716Hom.: 0 AF XY: 0.0000891 AC XY: 12AN XY: 134732
GnomAD4 exome AF: 0.0000904 AC: 132AN: 1460612Hom.: 0 Cov.: 32 AF XY: 0.0000867 AC XY: 63AN XY: 726500
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74390
ClinVar
Submissions by phenotype
Specific granule deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at