rs7542294

Positions:

• chr1-203182048-G-A
• chr1-203182048-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.587+683C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,322 control chromosomes in the GnomAD database, including 7,833 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 (7832 hom., cov: 32)
  • Exomes 𝑓: 0.099 (1 hom.)
• Consequence: CHI3L1 NM_001276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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 = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHI3L1	NM_001276.4	c.587+683C>T		intron_variant		ENST00000255409.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L1	ENST00000255409.8	c.587+683C>T		intron_variant		1	NM_001276.4	P1
CHI3L1	ENST00000404436.2	c.75+683C>T		intron_variant		2
CHI3L1	ENST00000473185.1	n.87C>T		non_coding_transcript_exon_variant	1/2	2
CHI3L1	ENST00000472064.1	n.111+683C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42328 AN: 151974 Hom.: 7813 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.261

GnomAD4 exome AF: 0.0991 AC: 23 AN: 232 Hom.: 1 Cov.: 0 AF XY: 0.107 AC XY: 13 AN XY: 122

Gnomad4 AMR exome AF: 0.100

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.0957

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.279 AC: 42377 AN: 152090 Hom.: 7832 Cov.: 32 AF XY: 0.279 AC XY: 20715 AN XY: 74362

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.258

Alfa AF: 0.177 Hom.: 5659

Bravo AF: 0.312

Asia WGS AF: 0.337 AC: 1168 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	2.9
DANN	Benign	0.62

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: rs7542294; hg19: chr1-203151176;