chr12-51346629-G-GT
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001971.6(CELA1):c.9_10insA(p.Leu4fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000203 in 1,475,946 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
CELA1
NM_001971.6 frameshift
NM_001971.6 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.131
Genes affected
CELA1 (HGNC:3308): (chymotrypsin like elastase 1) 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, pancreatic elastase 1 is not expressed in the pancreas. To date, elastase 1 expression has only been detected in skin keratinocytes. Clinical literature that describes human elastase 1 activity in the pancreas or fecal material is actually referring to chymotrypsin-like elastase family, member 3B. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CELA1 | NM_001971.6 | c.9_10insA | p.Leu4fs | frameshift_variant | 1/8 | ENST00000293636.2 | NP_001962.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CELA1 | ENST00000293636.2 | c.9_10insA | p.Leu4fs | frameshift_variant | 1/8 | 1 | NM_001971.6 | ENSP00000293636.1 |
Frequencies
GnomAD3 genomes 0.000113 AC: 6AN: 53088Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.00000751 AC: 1AN: 133074Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 73130
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GnomAD4 exome AF: 0.0000169 AC: 24AN: 1422816Hom.: 0 Cov.: 34 AF XY: 0.0000155 AC XY: 11AN XY: 709764
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GnomAD4 genome 0.000113 AC: 6AN: 53130Hom.: 0 Cov.: 0 AF XY: 0.0000388 AC XY: 1AN XY: 25802
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at