dbSNP rs942694: CHI3L2:c.1035+73T>C (chr1-111241516-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004000.3(CHI3L2):c.1035+73T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 794,358 control chromosomes in the GnomAD database, including 34,627 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 ( 5571 hom., cov: 31)

Exomes 𝑓: 0.29 ( 29056 hom. )

Consequence

CHI3L2
NM_004000.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0380

Publications

8 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004000.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHI3L2	NM_004000.3	MANE Select	c.1035+73T>C	intron	N/A	NP_003991.2	Q15782-4
CHI3L2	NM_001025197.1		c.1005+73T>C	intron	N/A	NP_001020368.1	Q15782-6
CHI3L2	NM_001025199.2		c.798+73T>C	intron	N/A	NP_001020370.1	Q15782-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHI3L2	ENST00000369748.9	TSL:1 MANE Select	c.1035+73T>C	intron	N/A	ENSP00000358763.4	Q15782-4
CHI3L2	ENST00000466741.5	TSL:1	c.798+73T>C	intron	N/A	ENSP00000437086.1	Q15782-5
CHI3L2	ENST00000445067.6	TSL:5	c.1035+73T>C	intron	N/A	ENSP00000437082.1	Q15782-4

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37895

AN:

151922

Hom.:

5576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0971

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.276

GnomAD4 exome

AF:

0.291

AC:

186893

AN:

642318

Hom.:

29056

AF XY:

0.291

AC XY:

99199

AN XY:

340862

show subpopulations

African (AFR)

AF:

0.0925

AC:

1617

AN:

17476

American (AMR)

AF:

0.159

AC:

5386

AN:

33774

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

5508

AN:

16774

East Asian (EAS)

AF:

0.172

AC:

6151

AN:

35658

South Asian (SAS)

AF:

0.222

AC:

12947

AN:

58256

European-Finnish (FIN)

AF:

0.341

AC:

16920

AN:

49686

Middle Eastern (MID)

AF:

0.267

AC:

1071

AN:

4008

European-Non Finnish (NFE)

AF:

0.323

AC:

127330

AN:

393924

Other (OTH)

AF:

0.304

AC:

9963

AN:

32762

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

6098

12196

18294

24392

30490

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1428

2856

4284

5712

7140

<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:

0.249

AC:

37887

AN:

152040

Hom.:

5571

Cov.:

AF XY:

0.245

AC XY:

18232

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0968

AC:

4020

AN:

41512

American (AMR)

AF:

0.215

AC:

3283

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1203

AN:

3466

East Asian (EAS)

AF:

0.199

AC:

1030

AN:

5172

South Asian (SAS)

AF:

0.239

AC:

1151

AN:

4818

European-Finnish (FIN)

AF:

0.322

AC:

3395

AN:

10544

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.338

AC:

22963

AN:

67940

Other (OTH)

AF:

0.275

AC:

579

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1376

2751

4127

5502

6878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<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:

0.302

Hom.:

10015

Bravo

AF:

0.233

Asia WGS

AF:

0.238

AC:

829

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.6

(source)

DANN

Benign

0.57

PhyloP100

-0.038

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over