chr1-15462752-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_033440.3(CELA2A):​c.247G>A​(p.Val83Met) variant causes a missense change. The variant allele was found at a frequency of 0.00121 in 1,614,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00097 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 1 hom. )

Consequence

CELA2A
NM_033440.3 missense

Scores

3
11
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.55
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.1979923).
BS2
High AC in GnomAd4 at 148 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CELA2ANM_033440.3 linkuse as main transcriptc.247G>A p.Val83Met missense_variant 4/8 ENST00000359621.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CELA2AENST00000359621.5 linkuse as main transcriptc.247G>A p.Val83Met missense_variant 4/81 NM_033440.3 P1
CELA2AENST00000459653.1 linkuse as main transcriptn.273G>A non_coding_transcript_exon_variant 4/42

Frequencies

GnomAD3 genomes
AF:
0.000973
AC:
148
AN:
152082
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000579
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000579
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000568
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00163
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000597
AC:
150
AN:
251256
Hom.:
1
AF XY:
0.000619
AC XY:
84
AN XY:
135798
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.000202
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000462
Gnomad NFE exome
AF:
0.00107
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.00124
AC:
1810
AN:
1461830
Hom.:
1
Cov.:
33
AF XY:
0.00121
AC XY:
880
AN XY:
727212
show subpopulations
Gnomad4 AFR exome
AF:
0.000149
Gnomad4 AMR exome
AF:
0.000201
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000562
Gnomad4 NFE exome
AF:
0.00155
Gnomad4 OTH exome
AF:
0.000662
GnomAD4 genome
AF:
0.000972
AC:
148
AN:
152200
Hom.:
0
Cov.:
32
AF XY:
0.00101
AC XY:
75
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.000578
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000581
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000568
Gnomad4 NFE
AF:
0.00163
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00136
Hom.:
0
Bravo
AF:
0.000922
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00140
AC:
12
ExAC
AF:
0.000519
AC:
63
EpiCase
AF:
0.00115
EpiControl
AF:
0.00130

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 02, 2021The c.247G>A (p.V83M) alteration is located in exon 4 (coding exon 4) of the CELA2A gene. This alteration results from a G to A substitution at nucleotide position 247, causing the valine (V) at amino acid position 83 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.80
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Uncertain
0.020
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.77
D
Eigen
Uncertain
0.36
Eigen_PC
Benign
0.17
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.95
D
M_CAP
Benign
0.037
D
MetaRNN
Benign
0.20
T
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.9
M
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.51
T
PROVEAN
Uncertain
-2.8
D
REVEL
Pathogenic
0.71
Sift
Uncertain
0.025
D
Sift4G
Uncertain
0.034
D
Polyphen
1.0
D
Vest4
0.41
MVP
0.78
MPC
0.96
ClinPred
0.051
T
GERP RS
4.1
Varity_R
0.22
gMVP
0.80

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.

Other links and lift over

dbSNP: rs148630095; hg19: chr1-15789247; COSMIC: COSV62747836; COSMIC: COSV62747836; API