rs2275353

chr1-203181080-G-Achr1-203181080-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001276.4(CHI3L1):c.711+82C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,554,482 control chromosomes in the GnomAD database, including 36,373 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 (7748 hom., cov: 32)
  • Exomes 𝑓: 0.18 (28625 hom.)
• Consequence: CHI3L1 NM_001276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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]

ACMG classification

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 = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHI3L1	NM_001276.4	c.711+82C>T		intron_variant		ENST00000255409.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L1	ENST00000255409.8	c.711+82C>T		intron_variant		1	NM_001276.4	P1
CHI3L1	ENST00000404436.2	c.199+82C>T		intron_variant		2
CHI3L1	ENST00000472064.1	n.235+82C>T		intron_variant, non_coding_transcript_variant		2
CHI3L1	ENST00000473185.1	n.973+82C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42097 AN: 151968 Hom.: 7729 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0945

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.181 AC: 253808 AN: 1402396 Hom.: 28625 AF XY: 0.180 AC XY: 125036 AN XY: 695448

Gnomad4 AFR exome AF: 0.506

Gnomad4 AMR exome AF: 0.407

Gnomad4 ASJ exome AF: 0.227

Gnomad4 EAS exome AF: 0.432

Gnomad4 SAS exome AF: 0.219

Gnomad4 FIN exome AF: 0.0946

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.277 AC: 42146 AN: 152086 Hom.: 7748 Cov.: 32 AF XY: 0.277 AC XY: 20596 AN XY: 74360

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0945

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.257

Alfa AF: 0.215 Hom.: 1033

Bravo AF: 0.310

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.49
Dann	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2275353; hg19: chr1-203150208; COSMIC: COSV55137942; COSMIC: COSV55137942;