rs121912777
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_001025195.2(CES1):c.428G>T(p.Gly143Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G143E) has been classified as Pathogenic.
Frequency
Consequence
NM_001025195.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.428G>T | p.Gly143Val | missense_variant | 4/14 | ENST00000360526.8 | |
CES1 | NM_001025194.2 | c.425G>T | p.Gly142Val | missense_variant | 4/14 | ||
CES1 | NM_001266.5 | c.425G>T | p.Gly142Val | missense_variant | 4/14 | ||
CES1 | XM_005255774.3 | c.428G>T | p.Gly143Val | missense_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES1 | ENST00000360526.8 | c.428G>T | p.Gly143Val | missense_variant | 4/14 | 1 | NM_001025195.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 39
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251250Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135802
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000164 AC: 24AN: 1461698Hom.: 0 Cov.: 35 AF XY: 0.0000151 AC XY: 11AN XY: 727160
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152296Hom.: 0 Cov.: 39 AF XY: 0.0000269 AC XY: 2AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at