1-111229743-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001025199.2(CHI3L2):​c.-306G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,412,358 control chromosomes in the GnomAD database, including 1,165 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 0.054 ( 622 hom., cov: 29)
Exomes 𝑓: 0.0083 ( 543 hom. )

Consequence

CHI3L2
NM_001025199.2 5_prime_UTR_premature_start_codon_gain

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHI3L2NM_004000.3 linkuse as main transcriptc.41-109G>T intron_variant ENST00000369748.9 NP_003991.2 Q15782-4
CHI3L2NM_001025199.2 linkuse as main transcriptc.-306G>T 5_prime_UTR_premature_start_codon_gain_variant 1/10 NP_001020370.1 Q15782-5
CHI3L2NM_001025199.2 linkuse as main transcriptc.-306G>T 5_prime_UTR_variant 1/10 NP_001020370.1 Q15782-5
CHI3L2NM_001025197.1 linkuse as main transcriptc.41-999G>T intron_variant NP_001020368.1 Q15782-6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHI3L2ENST00000369748.9 linkuse as main transcriptc.41-109G>T intron_variant 1 NM_004000.3 ENSP00000358763.4 Q15782-4

Frequencies

GnomAD3 genomes
AF:
0.0535
AC:
7667
AN:
143434
Hom.:
616
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.177
Gnomad AMI
AF:
0.0102
Gnomad AMR
AF:
0.0254
Gnomad ASJ
AF:
0.00418
Gnomad EAS
AF:
0.0192
Gnomad SAS
AF:
0.0190
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0372
Gnomad NFE
AF:
0.00247
Gnomad OTH
AF:
0.0449
GnomAD4 exome
AF:
0.00830
AC:
10531
AN:
1268854
Hom.:
543
Cov.:
32
AF XY:
0.00816
AC XY:
5113
AN XY:
626730
show subpopulations
Gnomad4 AFR exome
AF:
0.187
Gnomad4 AMR exome
AF:
0.0139
Gnomad4 ASJ exome
AF:
0.00463
Gnomad4 EAS exome
AF:
0.0259
Gnomad4 SAS exome
AF:
0.0190
Gnomad4 FIN exome
AF:
0.0000437
Gnomad4 NFE exome
AF:
0.00178
Gnomad4 OTH exome
AF:
0.0188
GnomAD4 genome
AF:
0.0537
AC:
7701
AN:
143504
Hom.:
622
Cov.:
29
AF XY:
0.0530
AC XY:
3683
AN XY:
69532
show subpopulations
Gnomad4 AFR
AF:
0.177
Gnomad4 AMR
AF:
0.0251
Gnomad4 ASJ
AF:
0.00418
Gnomad4 EAS
AF:
0.0193
Gnomad4 SAS
AF:
0.0193
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00247
Gnomad4 OTH
AF:
0.0466
Alfa
AF:
0.0131
Hom.:
94
Bravo
AF:
0.0609
Asia WGS
AF:
0.0510
AC:
176
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
8.1
DANN
Benign
0.83

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

LitVar

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

Other links and lift over

dbSNP: rs12070867; hg19: chr1-111772365; API