rs11102221
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004000.3(CHI3L2):c.1036-33G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,612,402 control chromosomes in the GnomAD database, including 59,899 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 0.28 ( 6391 hom., cov: 32)
Exomes 𝑓: 0.27 ( 53508 hom. )
Consequence
CHI3L2
NM_004000.3 intron
NM_004000.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.476
Genes affected
CHI3L2 (HGNC:1933): (chitinase 3 like 2) The protein encoded by this gene is similar to bacterial chitinases but lacks chitinase activity. The encoded protein is secreted and is involved in cartilage biogenesis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHI3L2 | NM_004000.3 | c.1036-33G>A | intron_variant | ENST00000369748.9 | |||
CHI3L2 | NM_001025197.1 | c.1006-33G>A | intron_variant | ||||
CHI3L2 | NM_001025199.2 | c.799-33G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHI3L2 | ENST00000369748.9 | c.1036-33G>A | intron_variant | 1 | NM_004000.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 42982AN: 151944Hom.: 6372 Cov.: 32
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GnomAD3 exomes AF: 0.279 AC: 70040AN: 250864Hom.: 10744 AF XY: 0.275 AC XY: 37315AN XY: 135624
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GnomAD4 exome AF: 0.265 AC: 387363AN: 1460340Hom.: 53508 Cov.: 33 AF XY: 0.267 AC XY: 194044AN XY: 726548
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GnomAD4 genome ? AF: 0.283 AC: 43069AN: 152062Hom.: 6391 Cov.: 32 AF XY: 0.282 AC XY: 20972AN XY: 74332
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ClinVar
Not reported inComputational 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