chr1-15462809-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_033440.3(CELA2A):c.304G>T(p.Val102Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,614,088 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 4 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 30 hom. )
Consequence
CELA2A
NM_033440.3 missense
NM_033440.3 missense
Scores
5
7
6
Clinical Significance
Conservation
PhyloP100: 2.50
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.014178455).
BP6
Variant 1-15462809-G-T is Benign according to our data. Variant chr1-15462809-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3257603.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-15462809-G-T is described in Lovd as [Likely_benign].
BS2
High AC in GnomAd4 at 296 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELA2A | NM_033440.3 | c.304G>T | p.Val102Phe | missense_variant | 4/8 | ENST00000359621.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELA2A | ENST00000359621.5 | c.304G>T | p.Val102Phe | missense_variant | 4/8 | 1 | NM_033440.3 | P1 | |
CELA2A | ENST00000459653.1 | n.330G>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00195 AC: 297AN: 152100Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00330 AC: 829AN: 251472Hom.: 7 AF XY: 0.00360 AC XY: 489AN XY: 135906
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GnomAD4 exome AF: 0.00162 AC: 2367AN: 1461870Hom.: 30 Cov.: 33 AF XY: 0.00182 AC XY: 1326AN XY: 727232
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GnomAD4 genome AF: 0.00194 AC: 296AN: 152218Hom.: 4 Cov.: 33 AF XY: 0.00257 AC XY: 191AN XY: 74428
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | CELA2A: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Uncertain
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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at