1-21983722-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_007352.4(CELA3B):c.391C>T(p.Arg131Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00412 in 1,614,106 control chromosomes in the GnomAD database, including 211 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0031 ( 11 hom., cov: 32)
Exomes 𝑓: 0.0042 ( 200 hom. )
Consequence
CELA3B
NM_007352.4 missense
NM_007352.4 missense
Scores
1
10
7
Clinical Significance
Conservation
PhyloP100: -0.359
Genes affected
CELA3B (HGNC:15945): (chymotrypsin like elastase 3B) 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 3B has little elastolytic activity. Like most of the human elastases, elastase 3B 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 3B preferentially cleaves proteins after alanine residues. Elastase 3B 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, and excretion of this protein in fecal material is frequently used as a measure of pancreatic function in clinical assays. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.003702402).
BP6
Variant 1-21983722-C-T is Benign according to our data. Variant chr1-21983722-C-T is described in ClinVar as [Benign]. Clinvar id is 719065.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0512 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CELA3B | ENST00000337107.11 | c.391C>T | p.Arg131Cys | missense_variant | Exon 5 of 8 | 1 | NM_007352.4 | ENSP00000338369.6 | ||
CELA3B | ENST00000400277.2 | c.100C>T | p.Arg34Cys | missense_variant | Exon 2 of 5 | 5 | ENSP00000383135.2 | |||
CELA3B | ENST00000374666.1 | n.442C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 | |||||
ENSG00000285959 | ENST00000650360.1 | n.117C>T | non_coding_transcript_exon_variant | Exon 1 of 9 |
Frequencies
GnomAD3 genomes AF: 0.00313 AC: 476AN: 152154Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00884 AC: 2220AN: 251144Hom.: 74 AF XY: 0.0111 AC XY: 1507AN XY: 135730
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GnomAD4 exome AF: 0.00423 AC: 6179AN: 1461834Hom.: 200 Cov.: 73 AF XY: 0.00577 AC XY: 4194AN XY: 727222
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GnomAD4 genome AF: 0.00311 AC: 473AN: 152272Hom.: 11 Cov.: 32 AF XY: 0.00408 AC XY: 304AN XY: 74454
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Jan 30, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at