Genetic Variant NM_001276.4:c.587+683C>T (chr1-203182048-G-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_001276.4(CHI3L1):c.587+683C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,322 control chromosomes in the GnomAD database, including 7,833 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 0.28 ( 7832 hom., cov: 32)

Exomes 𝑓: 0.099 ( 1 hom. )

Consequence

CHI3L1
NM_001276.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470

Publications

13 publications found

Variant links:

Genes affected

CHI3L1 (HGNC:1932): (chitinase 3 like 1) Chitinases catalyze the hydrolysis of chitin, which is an abundant glycopolymer found in insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 family of chitinases includes eight human family members. This gene encodes a glycoprotein member of the glycosyl hydrolase 18 family. The protein lacks chitinase activity and is secreted by activated macrophages, chondrocytes, neutrophils and synovial cells. The protein is thought to play a role in the process of inflammation and tissue remodeling. [provided by RefSeq, Sep 2009]

CHI3L1 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

CHI3L1 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 (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHI3L1	NM_001276.4 link	c.587+683C>T		intron_variant	Intron 6 of 9	ENST00000255409.8	NP_001267.2	P36222A0A024R969

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CHI3L1	ENST00000255409.8 link	c.587+683C>T	intron_variant	Intron 6 of 9	1	NM_001276.4	ENSP00000255409.3	P36222
CHI3L1	ENST00000473185.1 link	n.87C>T	non_coding_transcript_exon_variant	Exon 1 of 2	2
CHI3L1	ENST00000404436.2 link	c.74+683C>T	intron_variant	Intron 1 of 3	2		ENSP00000385350.2	H0Y3U8
CHI3L1	ENST00000472064.1 link	n.111+683C>T	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42328

AN:

151974

Hom.:

7813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.0948

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.261

GnomAD4 exome

AF:

0.0991

AC:

AN:

232

Hom.:

Cov.:

AF XY:

0.107

AC XY:

AN XY:

122

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.100

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

European-Finnish (FIN)

AF:

0.143

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0957

AC:

AN:

188

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.546

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.279

AC:

42377

AN:

152090

Hom.:

7832

Cov.:

AF XY:

0.279

AC XY:

20715

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.500

AC:

20740

AN:

41458

American (AMR)

AF:

0.359

AC:

5479

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

816

AN:

3470

East Asian (EAS)

AF:

0.423

AC:

2188

AN:

5170

South Asian (SAS)

AF:

0.224

AC:

1077

AN:

4818

European-Finnish (FIN)

AF:

0.0948

AC:

1003

AN:

10584

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.152

AC:

10315

AN:

67992

Other (OTH)

AF:

0.258

AC:

546

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1372

2745

4117

5490

6862

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.199

Hom.:

12452

Bravo

AF:

0.312

Asia WGS

AF:

0.337

AC:

1168

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

2.9

(source)

DANN

Benign

0.62

PhyloP100

-0.047

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