rs11583210

chr1-111239264-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004000.3(CHI3L2):c.918+332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 222,596 control chromosomes in the GnomAD database, including 6,732 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 (4275 hom., cov: 32)
  • Exomes 𝑓: 0.26 (2457 hom.)
• Consequence: CHI3L2 NM_004000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHI3L2	NM_004000.3	c.918+332G>A		intron_variant		ENST00000369748.9
CHI3L2	NM_001025197.1	c.888+332G>A		intron_variant
CHI3L2	NM_001025199.2	c.681+332G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L2	ENST00000369748.9	c.918+332G>A		intron_variant		1	NM_004000.3	P1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34484 AN: 152020 Hom.: 4274 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.255 AC: 17994 AN: 70458 Hom.: 2457 Cov.: 0 AF XY: 0.260 AC XY: 9175 AN XY: 35276

Gnomad4 AFR exome AF: 0.145

Gnomad4 AMR exome AF: 0.326

Gnomad4 ASJ exome AF: 0.226

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.327

Gnomad4 FIN exome AF: 0.205

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.227 AC: 34515 AN: 152138 Hom.: 4275 Cov.: 32 AF XY: 0.226 AC XY: 16843 AN XY: 74388

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0969

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.214

Alfa AF: 0.257 Hom.: 1171

Bravo AF: 0.229

Asia WGS AF: 0.192 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	18
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.42		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.42		Position offset: -5

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

Publications

LitVar

Other links and lift over

dbSNP: rs11583210; hg19: chr1-111781886;