Variant 1-15482272-G-A 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.235G>A(p.Gly79Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,613,282 control chromosomes in the GnomAD database, including 58,965 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.27 ( 5882 hom., cov: 32)

Exomes 𝑓: 0.26 ( 53083 hom. )

Consequence

CELA2B
NM_015849.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75

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=3.6351685E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELA2B	NM_015849.3 link	c.235G>A	p.Gly79Arg	missense_variant	4/8	ENST00000375910.8	NP_056933.3	P08218Q6ISP9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CELA2B	ENST00000375910.8 link	c.235G>A	p.Gly79Arg	missense_variant	4/8	1	NM_015849.3	ENSP00000365075.3	P08218
CELA2B	ENST00000422901.1 link	c.292G>A	p.Gly98Arg	missense_variant	4/4	5		ENSP00000399811.1	Q5JRU4
CELA2B	ENST00000494280.1 link	n.584G>A		non_coding_transcript_exon_variant	5/6	5

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40713

AN:

151818

Hom.:

5876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.234

GnomAD3 exomes

AF:

0.281

AC:

70644

AN:

251032

Hom.:

11203

AF XY:

0.271

AC XY:

36788

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.267

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.562

Gnomad SAS exome

AF:

0.189

Gnomad FIN exome

AF:

0.281

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.246

GnomAD4 exome

AF:

0.261

AC:

382073

AN:

1461346

Hom.:

53083

Cov.:

AF XY:

0.258

AC XY:

187769

AN XY:

726972

show subpopulations

Gnomad4 AFR exome

AF:

0.256

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.158

Gnomad4 EAS exome

AF:

0.550

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.268

AC:

40738

AN:

151936

Hom.:

5882

Cov.:

AF XY:

0.270

AC XY:

20072

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.320

Gnomad4 ASJ

AF:

0.160

Gnomad4 EAS

AF:

0.559

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.252

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.254

Hom.:

13428

Bravo

AF:

0.272

TwinsUK

AF:

0.262

AC:

970

ALSPAC

AF:

0.250

AC:

965

ESP6500AA

AF:

0.261

AC:

1149

ESP6500EA

AF:

0.246

AC:

2113

ExAC

AF:

0.277

AC:

33583

Asia WGS

AF:

0.381

AC:

1326

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

0.30

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.33

CADD

Benign

0.090

DANN

Benign

0.26

DEOGEN2

Benign

0.13

T;T

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.00098

LIST_S2

Benign

0.12

T;T

MetaRNN

Benign

0.000036

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.28

N;.

PrimateAI

Benign

0.31

PROVEAN

Benign

4.2

N;N

REVEL

Uncertain

0.36

Sift

Benign

0.96

T;T

Sift4G

Benign

0.75

T;T

Polyphen

0.0

B;.

Vest4

0.051

MutPred

0.49

Gain of solvent accessibility (P = 0.0097);.;

MPC

0.36

ClinPred

0.00066

GERP RS

-6.2

Varity_R

0.047

gMVP

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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