16-55826168-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001025195.2(CES1):c.388A>G(p.Lys130Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.388A>G | p.Lys130Glu | missense_variant | 3/14 | ENST00000360526.8 | |
CES1 | NM_001025194.2 | c.385A>G | p.Lys129Glu | missense_variant | 3/14 | ||
CES1 | NM_001266.5 | c.385A>G | p.Lys129Glu | missense_variant | 3/14 | ||
CES1 | XM_005255774.3 | c.388A>G | p.Lys130Glu | missense_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES1 | ENST00000360526.8 | c.388A>G | p.Lys130Glu | missense_variant | 3/14 | 1 | NM_001025195.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251166Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135732
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461666Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727142
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.385A>G (p.K129E) alteration is located in exon 3 (coding exon 3) of the CES1 gene. This alteration results from a A to G substitution at nucleotide position 385, causing the lysine (K) at amino acid position 129 to be replaced by a glutamic acid (E). 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