Variant rs3766160 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015849.3(CELA2B):c.340G>A(p.Asp114Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,613,674 control chromosomes in the GnomAD database, including 57,479 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.26 ( 5616 hom., cov: 32)

Exomes 𝑓: 0.26 ( 51863 hom. )

Consequence

CELA2B
NM_015849.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

Variant links:

Genes affected

CELA2B (HGNC:29995): (chymotrypsin like elastase 2B) Elastases form a subfamily of serine proteases that hydrolyze many proteins in addition to elastin. Humans have six elastase genes which encode the structurally similar proteins elastase 1, 2, 2A, 2B, 3A, and 3B. Like most of the human elastases, elastase 2B is secreted from the pancreas as a zymogen. In other species, elastase 2B has been shown to preferentially cleave proteins after leucine, methionine, and phenylalanine residues. [provided by RefSeq, Jul 2008]

CELA2B 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 (MetaRNN=2.4650486E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELA2B	NM_015849.3 linkuse as main transcript	c.340G>A	p.Asp114Asn	missense_variant	4/8	ENST00000375910.8	NP_056933.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CELA2B	ENST00000375910.8 linkuse as main transcript	c.340G>A	p.Asp114Asn	missense_variant	4/8	1	NM_015849.3	ENSP00000365075	P1
CELA2B	ENST00000494280.1 linkuse as main transcript	n.689G>A		non_coding_transcript_exon_variant	5/6	5
CELA2B	ENST00000422901.1 linkuse as main transcript			downstream_gene_variant		5		ENSP00000399811

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39938

AN:

151940

Hom.:

5612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.229

GnomAD3 exomes

AF:

0.274

AC:

68796

AN:

251436

Hom.:

10478

AF XY:

0.265

AC XY:

36004

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.266

Gnomad AMR exome

AF:

0.323

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.547

Gnomad SAS exome

AF:

0.188

Gnomad FIN exome

AF:

0.275

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.240

GnomAD4 exome

AF:

0.259

AC:

378902

AN:

1461616

Hom.:

51863

Cov.:

AF XY:

0.256

AC XY:

186371

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.255

Gnomad4 AMR exome

AF:

0.317

Gnomad4 ASJ exome

AF:

0.158

Gnomad4 EAS exome

AF:

0.534

Gnomad4 SAS exome

AF:

0.195

Gnomad4 FIN exome

AF:

0.274

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.256

GnomAD4 genome

AF:

0.263

AC:

39955

AN:

152058

Hom.:

5616

Cov.:

AF XY:

0.264

AC XY:

19597

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.256

Gnomad4 AMR

AF:

0.284

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.542

Gnomad4 SAS

AF:

0.216

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.230

Alfa

AF:

0.253

Hom.:

12663

Bravo

AF:

0.265

TwinsUK

AF:

0.262

AC:

970

ALSPAC

AF:

0.250

AC:

965

ESP6500AA

AF:

0.261

AC:

1151

ESP6500EA

AF:

0.245

AC:

2111

ExAC

AF:

0.271

AC:

32906

Asia WGS

AF:

0.361

AC:

1256

AN:

3478

EpiCase

AF:

0.237

EpiControl

AF:

0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

1.2

DANN

Benign

0.37

DEOGEN2

Benign

0.12

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.00098

LIST_S2

Benign

0.042

MetaRNN

Benign

0.000025

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.46

MutationTaster

Benign

1.0

PrimateAI

Benign

0.29

PROVEAN

Benign

1.2

REVEL

Benign

0.13

Sift

Benign

1.0

Sift4G

Benign

0.67

Polyphen

0.0

Vest4

0.056

MPC

0.30

ClinPred

0.000016

GERP RS

0.47

Varity_R

0.037

gMVP

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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