chr1-21980883-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_007352.4(CELA3B):c.189C>T(p.Ile63Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00487 in 1,612,476 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0051 ( 10 hom., cov: 29)
Exomes 𝑓: 0.0048 ( 30 hom. )
Consequence
CELA3B
NM_007352.4 synonymous
NM_007352.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.30
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-21980883-C-T is Benign according to our data. Variant chr1-21980883-C-T is described in ClinVar as [Benign]. Clinvar id is 774391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.3 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CELA3B | ENST00000337107.11 | c.189C>T | p.Ile63Ile | synonymous_variant | Exon 3 of 8 | 1 | NM_007352.4 | ENSP00000338369.6 | ||
CELA3B | ENST00000374666.1 | n.240C>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 3 | |||||
CELA3B | ENST00000400277.2 | c.-219C>T | upstream_gene_variant | 5 | ENSP00000383135.2 |
Frequencies
GnomAD3 genomes AF: 0.00509 AC: 769AN: 151092Hom.: 10 Cov.: 29
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GnomAD3 exomes AF: 0.00493 AC: 1237AN: 250760Hom.: 7 AF XY: 0.00515 AC XY: 698AN XY: 135584
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GnomAD4 exome AF: 0.00485 AC: 7084AN: 1461266Hom.: 30 Cov.: 56 AF XY: 0.00485 AC XY: 3523AN XY: 726960
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GnomAD4 genome AF: 0.00507 AC: 766AN: 151210Hom.: 10 Cov.: 29 AF XY: 0.00542 AC XY: 400AN XY: 73852
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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
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at