Variant rs11583210 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.963

Variant links:

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]

CHI3L2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	MANE	Protein	UniProt
CHI3L2	NM_004000.3 link	c.918+332G>A	intron_variant	ENST00000369748.9	NP_003991.2	Q15782-4
CHI3L2	NM_001025197.1 link	c.888+332G>A	intron_variant		NP_001020368.1	Q15782-6
CHI3L2	NM_001025199.2 link	c.681+332G>A	intron_variant		NP_001020370.1	Q15782-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHI3L2	ENST00000369748.9 link	c.918+332G>A		intron_variant		1	NM_004000.3	ENSP00000358763.4		Q15782-4

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34484

AN:

152020

Hom.:

4274

Cov.:

show subpopulations

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.:

AF XY:

0.260

AC XY:

9175

AN XY:

35276

show subpopulations

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.:

AF XY:

0.226

AC XY:

16843

AN XY:

74388

show subpopulations

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over