16-55810697-G-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001025195.2(CES1):c.1171-33C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 1,591,444 control chromosomes in the GnomAD database, including 500,839 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.77 ( 45158 hom., cov: 34)
Exomes 𝑓: 0.79 ( 455681 hom. )
Consequence
CES1
NM_001025195.2 intron
NM_001025195.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.61
Genes affected
CES1 (HGNC:1863): (carboxylesterase 1) This gene encodes a member of the carboxylesterase large family. The family members are responsible for the hydrolysis or transesterification of various xenobiotics, such as cocaine and heroin, and endogenous substrates with ester, thioester, or amide bonds. They may participate in fatty acyl and cholesterol ester metabolism, and may play a role in the blood-brain barrier system. This enzyme is the major liver enzyme and functions in liver drug clearance. Mutations of this gene cause carboxylesterase 1 deficiency. Three transcript variants encoding three different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.1171-33C>A | intron_variant | Intron 10 of 13 | ENST00000360526.8 | NP_001020366.1 | ||
CES1 | NM_001025194.2 | c.1168-33C>A | intron_variant | Intron 10 of 13 | NP_001020365.1 | |||
CES1 | NM_001266.5 | c.1165-33C>A | intron_variant | Intron 10 of 13 | NP_001257.4 | |||
CES1 | XM_005255774.3 | c.1168-33C>A | intron_variant | Intron 10 of 13 | XP_005255831.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.769 AC: 115961AN: 150772Hom.: 45117 Cov.: 34
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GnomAD3 exomes AF: 0.732 AC: 182802AN: 249766Hom.: 68597 AF XY: 0.729 AC XY: 98482AN XY: 135056
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GnomAD4 exome AF: 0.789 AC: 1136927AN: 1440552Hom.: 455681 Cov.: 48 AF XY: 0.783 AC XY: 561852AN XY: 717270
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GnomAD4 genome AF: 0.769 AC: 116047AN: 150892Hom.: 45158 Cov.: 34 AF XY: 0.763 AC XY: 56268AN XY: 73710
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at