dbSNP rs10927792: CELA2B:p.Thr158Thr (chr1-15483381-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015849.3(CELA2B):c.474G>A(p.Thr158Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,613,732 control chromosomes in the GnomAD database, including 60,859 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 0.29 ( 6812 hom., cov: 32)

Exomes 𝑓: 0.26 ( 54047 hom. )

Consequence

CELA2B
NM_015849.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.05

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-6.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELA2B	NM_015849.3 link	c.474G>A	p.Thr158Thr	synonymous_variant	Exon 5 of 8	ENST00000375910.8	NP_056933.3	P08218Q6ISP9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELA2B	ENST00000375910.8 link	c.474G>A	p.Thr158Thr	synonymous_variant	Exon 5 of 8	1	NM_015849.3	ENSP00000365075.3		P08218
CELA2B	ENST00000494280.1 link	n.*13G>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43800

AN:

151998

Hom.:

6802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.250

GnomAD3 exomes

AF:

0.286

AC:

71799

AN:

250742

Hom.:

11561

AF XY:

0.275

AC XY:

37219

AN XY:

135514

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.366

Gnomad ASJ exome

AF:

0.157

Gnomad EAS exome

AF:

0.561

Gnomad SAS exome

AF:

0.189

Gnomad FIN exome

AF:

0.281

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.264

AC:

385415

AN:

1461616

Hom.:

54047

Cov.:

AF XY:

0.260

AC XY:

189191

AN XY:

727112

show subpopulations

Gnomad4 AFR exome

AF:

0.321

Gnomad4 AMR exome

AF:

0.361

Gnomad4 ASJ exome

AF:

0.159

Gnomad4 EAS exome

AF:

0.553

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.265

GnomAD4 genome

AF:

0.288

AC:

43842

AN:

152116

Hom.:

6812

Cov.:

AF XY:

0.290

AC XY:

21541

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.325

Gnomad4 AMR

AF:

0.328

Gnomad4 ASJ

AF:

0.161

Gnomad4 EAS

AF:

0.561

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.252

Gnomad4 OTH

AF:

0.251

Alfa

AF:

0.255

Hom.:

2168

Bravo

AF:

0.294

Asia WGS

AF:

0.386

AC:

1343

AN:

3478

EpiCase

AF:

0.237

EpiControl

AF:

0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.0090

DANN

Benign

0.85

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