rs1325284

Positions:

• chr1-111233170-A-G
• chr1-111233170-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004000.3(CHI3L2):​c.330-1737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,052 control chromosomes in the GnomAD database, including 5,588 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 0.25 (5588 hom., cov: 32)
• Consequence: CHI3L2 NM_004000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHI3L2	NM_004000.3	c.330-1737A>G		intron_variant		ENST00000369748.9
CHI3L2	NM_001025197.1	c.300-1737A>G		intron_variant
CHI3L2	NM_001025199.2	c.93-1737A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L2	ENST00000369748.9	c.330-1737A>G		intron_variant		1	NM_004000.3	P1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37959 AN: 151934 Hom.: 5593 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.277

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.250 AC: 37951 AN: 152052 Hom.: 5588 Cov.: 32 AF XY: 0.246 AC XY: 18259 AN XY: 74310

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.276

Alfa AF: 0.182 Hom.: 452

Bravo AF: 0.234

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	11
DANN	Benign	0.92

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: rs1325284; hg19: chr1-111775792;