Variant 16-55833094-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001025195.2(CES1):c.-39A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 1,359,412 control chromosomes in the GnomAD database, including 12,347 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 0.24 ( 3782 hom., cov: 32)

Exomes 𝑓: 0.035 ( 8565 hom. )

Consequence

CES1
NM_001025195.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.59

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]

CES1 links:

CES1 (HGNC:):

CES1 links:

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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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
CES1	NM_001025195.2 linkuse as main transcript	c.-39A>G	5_prime_UTR_variant	1/14	ENST00000360526.8	NP_001020366.1	P23141-2
CES1	NM_001025194.2 linkuse as main transcript	c.-39A>G	5_prime_UTR_variant	1/14		NP_001020365.1	P23141-1
CES1	NM_001266.5 linkuse as main transcript	c.-39A>G	5_prime_UTR_variant	1/14		NP_001257.4	P23141-3
CES1	XM_005255774.3 linkuse as main transcript	c.-39A>G	5_prime_UTR_variant	1/14		XP_005255831.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CES1	ENST00000360526.8 linkuse as main transcript	c.-39A>G		5_prime_UTR_variant	1/14	1	NM_001025195.2	ENSP00000353720.4		P23141-2

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

30760

AN:

125826

Hom.:

3778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.317

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.350

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.248

GnomAD3 exomes

AF:

0.0484

AC:

10381

AN:

214430

Hom.:

2513

AF XY:

0.0440

AC XY:

5122

AN XY:

116340

show subpopulations

Gnomad AFR exome

AF:

0.207

Gnomad AMR exome

AF:

0.0297

Gnomad ASJ exome

AF:

0.0591

Gnomad EAS exome

AF:

0.0671

Gnomad SAS exome

AF:

0.0312

Gnomad FIN exome

AF:

0.0275

Gnomad NFE exome

AF:

0.0360

Gnomad OTH exome

AF:

0.0499

GnomAD4 exome

AF:

0.0354

AC:

43609

AN:

1233492

Hom.:

8565

Cov.:

AF XY:

0.0360

AC XY:

22065

AN XY:

613338

show subpopulations

Gnomad4 AFR exome

AF:

0.189

Gnomad4 AMR exome

AF:

0.0335

Gnomad4 ASJ exome

AF:

0.0636

Gnomad4 EAS exome

AF:

0.0516

Gnomad4 SAS exome

AF:

0.0413

Gnomad4 FIN exome

AF:

0.0367

Gnomad4 NFE exome

AF:

0.0276

Gnomad4 OTH exome

AF:

0.0533

GnomAD4 genome

AF:

0.244

AC:

30781

AN:

125920

Hom.:

3782

Cov.:

AF XY:

0.241

AC XY:

14750

AN XY:

61134

show subpopulations

Gnomad4 AFR

AF:

0.317

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.206

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.221

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.212

Gnomad4 OTH

AF:

0.252

Alfa

AF:

0.103

Hom.:

252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.011

DANN

Benign

0.23

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over