chr1-203181051-G-A

Position:

• chr1-203181051-G-A

Variant summary

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

The NM_001276.4(CHI3L1):​c.711+111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,375,366 control chromosomes in the GnomAD database, including 32,528 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 (8068 hom., cov: 32)
  • Exomes 𝑓: 0.18 (24460 hom.)
• Consequence: CHI3L1 NM_001276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHI3L1	NM_001276.4	c.711+111C>T		intron_variant		ENST00000255409.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L1	ENST00000255409.8	c.711+111C>T		intron_variant		1	NM_001276.4	P1
CHI3L1	ENST00000404436.2	c.199+111C>T		intron_variant		2
CHI3L1	ENST00000472064.1	n.235+111C>T		intron_variant, non_coding_transcript_variant		2
CHI3L1	ENST00000473185.1	n.973+111C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42735 AN: 151980 Hom.: 8049 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.180 AC: 219738 AN: 1223268 Hom.: 24460 AF XY: 0.179 AC XY: 108059 AN XY: 604144

Gnomad4 AFR exome AF: 0.521

Gnomad4 AMR exome AF: 0.399

Gnomad4 ASJ exome AF: 0.226

Gnomad4 EAS exome AF: 0.435

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.0950

Gnomad4 NFE exome AF: 0.153

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.281 AC: 42786 AN: 152098 Hom.: 8068 Cov.: 32 AF XY: 0.281 AC XY: 20885 AN XY: 74374

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0947

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.259

Alfa AF: 0.262 Hom.: 1349

Bravo AF: 0.315

Asia WGS AF: 0.321 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.27

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: rs2275352; hg19: chr1-203150179; COSMIC: COSV55137032; COSMIC: COSV55137032;