chr1-203186575-A-T

Position:

• chr1-203186575-A-T

Variant summary

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

The ENST00000255409.8(CHI3L1):​c.25+24T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,613,380 control chromosomes in the GnomAD database, including 26,296 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 0.23 (5649 hom., cov: 29)
  • Exomes 𝑓: 0.15 (20647 hom.)
• Consequence: CHI3L1 ENST00000255409.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHI3L1	NM_001276.4	c.25+24T>A		intron_variant		ENST00000255409.8	NP_001267.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHI3L1	ENST00000255409.8	c.25+24T>A		intron_variant		1	NM_001276.4	ENSP00000255409	P1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35581 AN: 151772 Hom.: 5623 Cov.: 29

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0692

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.228

GnomAD3 exomes AF: 0.194 AC: 48704 AN: 251056 Hom.: 6350 AF XY: 0.180 AC XY: 24451 AN XY: 135730

Gnomad AFR exome AF: 0.446

Gnomad AMR exome AF: 0.355

Gnomad ASJ exome AF: 0.182

Gnomad EAS exome AF: 0.292

Gnomad SAS exome AF: 0.155

Gnomad FIN exome AF: 0.0717

Gnomad NFE exome AF: 0.128

Gnomad OTH exome AF: 0.183

GnomAD4 exome AF: 0.152 AC: 221631 AN: 1461490 Hom.: 20647 Cov.: 34 AF XY: 0.150 AC XY: 108820 AN XY: 727072

Gnomad4 AFR exome AF: 0.449

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.181

Gnomad4 EAS exome AF: 0.305

Gnomad4 SAS exome AF: 0.152

Gnomad4 FIN exome AF: 0.0733

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.235 AC: 35627 AN: 151890 Hom.: 5649 Cov.: 29 AF XY: 0.233 AC XY: 17329 AN XY: 74248

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0692

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.225

Alfa AF: 0.0975 Hom.: 185

Bravo AF: 0.265

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
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: rs7515776; hg19: chr1-203155703;