16-55810697-G-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61
Variant links:
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
CES1NM_001025195.2 linkc.1171-33C>A intron_variant Intron 10 of 13 ENST00000360526.8 NP_001020366.1 P23141-2
CES1NM_001025194.2 linkc.1168-33C>A intron_variant Intron 10 of 13 NP_001020365.1 P23141-1
CES1NM_001266.5 linkc.1165-33C>A intron_variant Intron 10 of 13 NP_001257.4 P23141-3
CES1XM_005255774.3 linkc.1168-33C>A intron_variant Intron 10 of 13 XP_005255831.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CES1ENST00000360526.8 linkc.1171-33C>A intron_variant Intron 10 of 13 1 NM_001025195.2 ENSP00000353720.4 P23141-2

Frequencies

GnomAD3 genomes
AF:
0.769
AC:
115961
AN:
150772
Hom.:
45117
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.755
Gnomad AMI
AF:
0.667
Gnomad AMR
AF:
0.762
Gnomad ASJ
AF:
0.770
Gnomad EAS
AF:
0.403
Gnomad SAS
AF:
0.592
Gnomad FIN
AF:
0.802
Gnomad MID
AF:
0.742
Gnomad NFE
AF:
0.816
Gnomad OTH
AF:
0.752
GnomAD3 exomes
AF:
0.732
AC:
182802
AN:
249766
Hom.:
68597
AF XY:
0.729
AC XY:
98482
AN XY:
135056
show subpopulations
Gnomad AFR exome
AF:
0.758
Gnomad AMR exome
AF:
0.687
Gnomad ASJ exome
AF:
0.776
Gnomad EAS exome
AF:
0.405
Gnomad SAS exome
AF:
0.596
Gnomad FIN exome
AF:
0.805
Gnomad NFE exome
AF:
0.813
Gnomad OTH exome
AF:
0.754
GnomAD4 exome
AF:
0.789
AC:
1136927
AN:
1440552
Hom.:
455681
Cov.:
48
AF XY:
0.783
AC XY:
561852
AN XY:
717270
show subpopulations
Gnomad4 AFR exome
AF:
0.764
Gnomad4 AMR exome
AF:
0.696
Gnomad4 ASJ exome
AF:
0.779
Gnomad4 EAS exome
AF:
0.400
Gnomad4 SAS exome
AF:
0.599
Gnomad4 FIN exome
AF:
0.808
Gnomad4 NFE exome
AF:
0.824
Gnomad4 OTH exome
AF:
0.763
GnomAD4 genome
AF:
0.769
AC:
116047
AN:
150892
Hom.:
45158
Cov.:
34
AF XY:
0.763
AC XY:
56268
AN XY:
73710
show subpopulations
Gnomad4 AFR
AF:
0.755
Gnomad4 AMR
AF:
0.762
Gnomad4 ASJ
AF:
0.770
Gnomad4 EAS
AF:
0.403
Gnomad4 SAS
AF:
0.591
Gnomad4 FIN
AF:
0.802
Gnomad4 NFE
AF:
0.816
Gnomad4 OTH
AF:
0.752
Alfa
AF:
0.794
Hom.:
56020
Bravo
AF:
0.762
Asia WGS
AF:
0.512
AC:
1783
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.21
DANN
Benign
0.67
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2244613; hg19: chr16-55844609; COSMIC: COSV62085645; COSMIC: COSV62085645; API