chr16-55819548-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001025195.2(CES1):c.893C>T(p.Thr298Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001025195.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.893C>T | p.Thr298Met | missense_variant | 7/14 | ENST00000360526.8 | |
CES1 | NM_001025194.2 | c.890C>T | p.Thr297Met | missense_variant | 7/14 | ||
CES1 | NM_001266.5 | c.890C>T | p.Thr297Met | missense_variant | 7/14 | ||
CES1 | XM_005255774.3 | c.893C>T | p.Thr298Met | missense_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES1 | ENST00000360526.8 | c.893C>T | p.Thr298Met | missense_variant | 7/14 | 1 | NM_001025195.2 | P4 | |
CES1 | ENST00000361503.8 | c.890C>T | p.Thr297Met | missense_variant | 7/14 | 1 | A1 | ||
CES1 | ENST00000422046.6 | c.890C>T | p.Thr297Met | missense_variant | 7/14 | 1 | A1 | ||
CES1 | ENST00000569260.1 | c.35C>T | p.Thr12Met | missense_variant, NMD_transcript_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251338Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135850
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461118Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726920
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.890C>T (p.T297M) alteration is located in exon 7 (coding exon 7) of the CES1 gene. This alteration results from a C to T substitution at nucleotide position 890, causing the threonine (T) at amino acid position 297 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at