rs1538372
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001276.4(CHI3L1):c.56-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 1,612,088 control chromosomes in the GnomAD database, including 350,973 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.67 ( 34340 hom., cov: 31)
Exomes 𝑓: 0.66 ( 316633 hom. )
Consequence
CHI3L1
NM_001276.4 intron
NM_001276.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.617
Genes affected
CHI3L1 (HGNC:1932): (chitinase 3 like 1) Chitinases catalyze the hydrolysis of chitin, which is an abundant glycopolymer found in insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 family of chitinases includes eight human family members. This gene encodes a glycoprotein member of the glycosyl hydrolase 18 family. The protein lacks chitinase activity and is secreted by activated macrophages, chondrocytes, neutrophils and synovial cells. The protein is thought to play a role in the process of inflammation and tissue remodeling. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHI3L1 | NM_001276.4 | c.56-19T>C | intron_variant | ENST00000255409.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHI3L1 | ENST00000255409.8 | c.56-19T>C | intron_variant | 1 | NM_001276.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.671 AC: 101996AN: 151906Hom.: 34309 Cov.: 31
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GnomAD3 exomes AF: 0.651 AC: 163038AN: 250254Hom.: 53254 AF XY: 0.649 AC XY: 87892AN XY: 135336
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GnomAD4 exome AF: 0.658 AC: 960649AN: 1460062Hom.: 316633 Cov.: 35 AF XY: 0.656 AC XY: 476718AN XY: 726374
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GnomAD4 genome ? AF: 0.671 AC: 102068AN: 152026Hom.: 34340 Cov.: 31 AF XY: 0.670 AC XY: 49778AN XY: 74312
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ClinVar
Not reported inComputational scores
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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