16-55826236-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001025195.2(CES1):āc.320A>Gā(p.Glu107Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001025195.2 missense
Scores
Clinical Significance
Conservation
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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.320A>G | p.Glu107Gly | missense_variant | 3/14 | ENST00000360526.8 | |
CES1 | NM_001025194.2 | c.317A>G | p.Glu106Gly | missense_variant | 3/14 | ||
CES1 | NM_001266.5 | c.317A>G | p.Glu106Gly | missense_variant | 3/14 | ||
CES1 | XM_005255774.3 | c.320A>G | p.Glu107Gly | missense_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES1 | ENST00000360526.8 | c.320A>G | p.Glu107Gly | missense_variant | 3/14 | 1 | NM_001025195.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251178Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135742
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461654Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727134
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.317A>G (p.E106G) 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 317, causing the glutamic acid (E) at amino acid position 106 to be replaced by a glycine (G). 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