dbSNP rs11583210: CHI3L2:c.918+332G>A (chr1-111239264-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

1 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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	Exon rank	MANE	Protein	UniProt
CHI3L2	NM_004000.3 link	c.918+332G>A	intron_variant	Intron 8 of 10	ENST00000369748.9	NP_003991.2	Q15782-4
CHI3L2	NM_001025197.1 link	c.888+332G>A	intron_variant	Intron 7 of 9		NP_001020368.1	Q15782-6
CHI3L2	NM_001025199.2 link	c.681+332G>A	intron_variant	Intron 7 of 9		NP_001020370.1	Q15782-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHI3L2	ENST00000369748.9 link	c.918+332G>A		intron_variant	Intron 8 of 10	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

African (AFR)

AF:

0.145

AC:

263

AN:

1818

American (AMR)

AF:

0.326

AC:

513

AN:

1574

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

581

AN:

2574

East Asian (EAS)

AF:

0.101

AC:

325

AN:

3204

South Asian (SAS)

AF:

0.327

AC:

1288

AN:

3938

European-Finnish (FIN)

AF:

0.205

AC:

824

AN:

4014

Middle Eastern (MID)

AF:

0.276

AC:

118

AN:

428

European-Non Finnish (NFE)

AF:

0.270

AC:

12908

AN:

47842

Other (OTH)

AF:

0.232

AC:

1174

AN:

5066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

653

1306

1960

2613

3266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.227

AC:

34515

AN:

152138

Hom.:

4275

Cov.:

AF XY:

0.226

AC XY:

16843

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.143

AC:

5915

AN:

41500

American (AMR)

AF:

0.294

AC:

4489

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

811

AN:

3466

East Asian (EAS)

AF:

0.0969

AC:

502

AN:

5182

South Asian (SAS)

AF:

0.304

AC:

1464

AN:

4808

European-Finnish (FIN)

AF:

0.197

AC:

2086

AN:

10602

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.272

AC:

18469

AN:

67982

Other (OTH)

AF:

0.214

AC:

453

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1370

2740

4111

5481

6851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.255

Hom.:

1183

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

(source)

DANN

Benign

0.79

PhyloP100

-0.96

PromoterAI

0.011

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over