Genetic Variant CES4A:p.Ala453Thr (chr16-67006432-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001364782.1(CES4A):c.1357G>A(p.Ala453Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0172 in 1,536,428 control chromosomes in the GnomAD database, including 2,673 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.078 ( 1453 hom., cov: 32)

Exomes 𝑓: 0.011 ( 1220 hom. )

Consequence

CES4A
NM_001364782.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.113

Publications

9 publications found

Variant links:

Genes affected

CES4A (HGNC:26741): (carboxylesterase 4A) 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 also participate in fatty acyl and cholesterol ester metabolism, and may play a role in the blood-brain barrier system. This gene, also called CES6, encodes a secreted enzyme, and may play a role in the detoxification of drugs and xenobiotics in neural and other tissues of the body and in the cerebrospinal fluid. Multiple transcript variants encoding different isoforms have been reported, but the full-length nature and/or biological validity of some variants have not been determined. [provided by RefSeq, Jun 2010]

CES4A links:

ENSG00000280334 (HGNC:):

ENSG00000280334 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0046688616).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364782.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CES4A	NM_001364782.1	MANE Select	c.1357G>A	p.Ala453Thr	missense	Exon 12 of 14	NP_001351711.1
CES4A	NM_001190201.2		c.1063G>A	p.Ala355Thr	missense	Exon 10 of 12	NP_001177130.1
CES4A	NM_001318506.2		c.775G>A	p.Ala259Thr	missense	Exon 10 of 12	NP_001305435.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CES4A	ENST00000648724.3	MANE Select	c.1357G>A	p.Ala453Thr	missense	Exon 12 of 14	ENSP00000497868.2
CES4A	ENST00000540579.6	TSL:1	c.1063G>A	p.Ala355Thr	missense	Exon 10 of 12	ENSP00000441907.1
CES4A	ENST00000538199.5	TSL:1	c.1124-313G>A		intron	N/A	ENSP00000441103.1

Frequencies

GnomAD3 genomes

AF:

0.0783

AC:

11907

AN:

152024

Hom.:

1452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0298

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00453

Gnomad OTH

AF:

0.0570

GnomAD2 exomes

AF:

0.0195

AC:

2714

AN:

139408

AF XY:

0.0152

show subpopulations

Gnomad AFR exome

AF:

0.274

Gnomad AMR exome

AF:

0.0153

Gnomad ASJ exome

AF:

0.0178

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000140

Gnomad NFE exome

AF:

0.00433

Gnomad OTH exome

AF:

0.0109

GnomAD4 exome

AF:

0.0105

AC:

14560

AN:

1384286

Hom.:

1220

Cov.:

AF XY:

0.00950

AC XY:

6489

AN XY:

683068

show subpopulations

African (AFR)

AF:

0.267

AC:

8423

AN:

31582

American (AMR)

AF:

0.0181

AC:

646

AN:

35700

Ashkenazi Jewish (ASJ)

AF:

0.0175

AC:

440

AN:

25178

East Asian (EAS)

AF:

0.00

AC:

AN:

35734

South Asian (SAS)

AF:

0.00187

AC:

148

AN:

79238

European-Finnish (FIN)

AF:

0.000322

AC:

AN:

34144

Middle Eastern (MID)

AF:

0.0158

AC:

AN:

5700

European-Non Finnish (NFE)

AF:

0.00332

AC:

3584

AN:

1078956

Other (OTH)

AF:

0.0210

AC:

1218

AN:

58054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

616

1232

1847

2463

3079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

306

612

918

1224

1530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0784

AC:

11925

AN:

152142

Hom.:

1453

Cov.:

AF XY:

0.0760

AC XY:

5651

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.265

AC:

10961

AN:

41430

American (AMR)

AF:

0.0297

AC:

454

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0167

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.00331

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0000942

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00454

AC:

309

AN:

68010

Other (OTH)

AF:

0.0564

AC:

119

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

457

913

1370

1826

2283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0304

Hom.:

1301

Bravo

AF:

0.0884

TwinsUK

AF:

0.00620

AC:

ALSPAC

AF:

0.00337

AC:

ExAC

AF:

0.0140

AC:

466

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.44

(source)

DANN

Benign

0.97

Eigen

Benign

-0.97

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.025

LIST_S2

Benign

0.39

MetaRNN

Benign

0.0047

MetaSVM

Benign

-1.0

PhyloP100

-0.11

PROVEAN

Benign

-0.30

REVEL

Benign

0.040

Sift

Benign

0.041

Sift4G

Uncertain

0.0060

Vest4

0.018

ClinPred

0.0020

GERP RS

-1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over