1-22007501-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005747.5(CELA3A):​c.628C>T​(p.Arg210Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,610,144 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 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000032 ( 1 hom. )

Consequence

CELA3A
NM_005747.5 missense

Scores

6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.337
Variant links:
Genes affected
CELA3A (HGNC:15944): (chymotrypsin like elastase 3A) 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. Unlike other elastases, elastase 3A has little elastolytic activity. Like most of the human elastases, elastase 3A is secreted from the pancreas as a zymogen and, like other serine proteases such as trypsin, chymotrypsin and kallikrein, it has a digestive function in the intestine. Elastase 3A preferentially cleaves proteins after alanine residues. Elastase 3A may also function in the intestinal transport and metabolism of cholesterol. Both elastase 3A and elastase 3B have been referred to as protease E and as elastase 1. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2111781).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CELA3ANM_005747.5 linkc.628C>T p.Arg210Cys missense_variant Exon 6 of 8 ENST00000290122.8 NP_005738.4 P09093

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CELA3AENST00000290122.8 linkc.628C>T p.Arg210Cys missense_variant Exon 6 of 8 1 NM_005747.5 ENSP00000290122.3 P09093
CELA3AENST00000400271.2 linkc.52C>T p.Arg18Cys missense_variant Exon 1 of 4 3 ENSP00000383130.2 B1AQ55
ENSG00000285959ENST00000650360.1 linkn.883C>T non_coding_transcript_exon_variant Exon 6 of 9
ENSG00000285959ENST00000648697.1 linkn.240+1957C>T intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.0000594
AC:
9
AN:
151486
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000976
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000589
Gnomad OTH
AF:
0.000481
GnomAD3 exomes
AF:
0.0000361
AC:
9
AN:
249484
Hom.:
0
AF XY:
0.0000297
AC XY:
4
AN XY:
134902
show subpopulations
Gnomad AFR exome
AF:
0.000124
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000165
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000266
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.0000315
AC:
46
AN:
1458658
Hom.:
1
Cov.:
31
AF XY:
0.0000289
AC XY:
21
AN XY:
725656
show subpopulations
Gnomad4 AFR exome
AF:
0.0000904
Gnomad4 AMR exome
AF:
0.0000225
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000355
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000198
Gnomad4 OTH exome
AF:
0.0000830
GnomAD4 genome
AF:
0.0000594
AC:
9
AN:
151486
Hom.:
0
Cov.:
32
AF XY:
0.0000405
AC XY:
3
AN XY:
73994
show subpopulations
Gnomad4 AFR
AF:
0.0000976
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000589
Gnomad4 OTH
AF:
0.000481
Bravo
AF:
0.0000982
ESP6500AA
AF:
0.000455
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000412
AC:
5

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 07, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.628C>T (p.R210C) alteration is located in exon 6 (coding exon 6) of the CELA3A gene. This alteration results from a C to T substitution at nucleotide position 628, causing the arginine (R) at amino acid position 210 to be replaced by a cysteine (C). 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
Uncertain
0.52
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.14
CADD
Benign
18
DANN
Uncertain
1.0
DEOGEN2
Benign
0.33
T;.
Eigen
Benign
-0.79
Eigen_PC
Benign
-0.91
FATHMM_MKL
Benign
0.12
N
LIST_S2
Uncertain
0.88
D;D
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.21
T;T
MetaSVM
Benign
-0.33
T
MutationAssessor
Uncertain
2.6
M;.
PROVEAN
Uncertain
-2.4
N;D
REVEL
Uncertain
0.42
Sift
Benign
0.051
T;T
Sift4G
Benign
0.062
T;D
Polyphen
0.14
B;.
Vest4
0.30
MVP
0.73
MPC
0.39
ClinPred
0.13
T
GERP RS
0.56
Varity_R
0.15
gMVP
0.71

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: rs149807589; hg19: chr1-22333994; COSMIC: COSV51586524; COSMIC: COSV51586524; API