dbSNP rs8535: CHI3L2:c.*93C>A (chr1-111243307-C-A) – 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.*93C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 453,778 control chromosomes in the GnomAD database, including 17,622 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 0.24 ( 5094 hom., cov: 33)

Exomes 𝑓: 0.28 ( 12528 hom. )

Consequence

CHI3L2
NM_004000.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.845

Publications

12 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CHI3L2	NM_004000.3 link	c.*93C>A	3_prime_UTR_variant	Exon 11 of 11	ENST00000369748.9	NP_003991.2	Q15782-4
CHI3L2	NM_001025197.1 link	c.*93C>A	3_prime_UTR_variant	Exon 10 of 10		NP_001020368.1	Q15782-6
CHI3L2	NM_001025199.2 link	c.*93C>A	3_prime_UTR_variant	Exon 10 of 10		NP_001020370.1	Q15782-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHI3L2	ENST00000369748.9 link	c.*93C>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_004000.3	ENSP00000358763.4		Q15782-4

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

37024

AN:

152078

Hom.:

5087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.290

Gnomad OTH

AF:

0.284

GnomAD4 exome

AF:

0.283

AC:

85279

AN:

301582

Hom.:

12528

Cov.:

AF XY:

0.282

AC XY:

48343

AN XY:

171632

show subpopulations

African (AFR)

AF:

0.103

AC:

883

AN:

8542

American (AMR)

AF:

0.309

AC:

8389

AN:

27144

Ashkenazi Jewish (ASJ)

AF:

0.390

AC:

4162

AN:

10674

East Asian (EAS)

AF:

0.347

AC:

3182

AN:

9172

South Asian (SAS)

AF:

0.253

AC:

15087

AN:

59538

European-Finnish (FIN)

AF:

0.254

AC:

3131

AN:

12322

Middle Eastern (MID)

AF:

0.375

AC:

977

AN:

2608

European-Non Finnish (NFE)

AF:

0.289

AC:

45436

AN:

157472

Other (OTH)

AF:

0.286

AC:

4032

AN:

14110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

3050

6099

9149

12198

15248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.243

AC:

37023

AN:

152196

Hom.:

5094

Cov.:

AF XY:

0.245

AC XY:

18195

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.114

AC:

4751

AN:

41548

American (AMR)

AF:

0.301

AC:

4599

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

1255

AN:

3470

East Asian (EAS)

AF:

0.327

AC:

1686

AN:

5162

South Asian (SAS)

AF:

0.244

AC:

1175

AN:

4822

European-Finnish (FIN)

AF:

0.257

AC:

2716

AN:

10584

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.290

AC:

19727

AN:

67996

Other (OTH)

AF:

0.281

AC:

593

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1439

2878

4317

5756

7195

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

390

780

1170

1560

1950

<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:

0.140

Hom.:

257

Bravo

AF:

0.244

Asia WGS

AF:

0.258

AC:

898

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.0

(source)

DANN

Benign

0.72

PhyloP100

-0.84

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over