Variant rs2901964 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000359621.5(CELA2A):c.494-68C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,569,754 control chromosomes in the GnomAD database, including 45,287 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 0.32 ( 11165 hom., cov: 31)

Exomes 𝑓: 0.20 ( 34122 hom. )

Consequence

CELA2A
ENST00000359621.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Variant links:

Genes affected

CELA2A (HGNC:24609): (chymotrypsin like elastase 2A) 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 2A is secreted from the pancreas as a zymogen. In other species, elastase 2A has been shown to preferentially cleave proteins after leucine, methionine, and phenylalanine residues. [provided by RefSeq, May 2009]

CELA2A links:

LOC105376767 (HGNC:):

LOC105376767 links:

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 (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELA2A	NM_033440.3 linkuse as main transcript	c.494-68C>G		intron_variant		ENST00000359621.5	NP_254275.1
LOC105376767	XR_002958256.2 linkuse as main transcript	n.367-1059G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CELA2A	ENST00000359621.5 linkuse as main transcript	c.494-68C>G		intron_variant		1	NM_033440.3	ENSP00000352639	P1
CELA2B	ENST00000494280.1 linkuse as main transcript	n.23C>G		non_coding_transcript_exon_variant	1/6	5

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48950

AN:

151904

Hom.:

11136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.647

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.0765

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.312

GnomAD4 exome

AF:

0.205

AC:

290259

AN:

1417732

Hom.:

34122

Cov.:

AF XY:

0.204

AC XY:

144363

AN XY:

706034

show subpopulations

Gnomad4 AFR exome

AF:

0.652

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.245

Gnomad4 EAS exome

AF:

0.0872

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.207

Gnomad4 NFE exome

AF:

0.196

Gnomad4 OTH exome

AF:

0.224

GnomAD4 genome

AF:

0.322

AC:

49027

AN:

152022

Hom.:

11165

Cov.:

AF XY:

0.317

AC XY:

23527

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.647

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.233

Gnomad4 EAS

AF:

0.0768

Gnomad4 SAS

AF:

0.183

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.310

Alfa

AF:

0.193

Hom.:

1777

Bravo

AF:

0.339

Asia WGS

AF:

0.186

AC:

644

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.83

DANN

Benign

0.39

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