rs12032329

Variant names:

• chr1-111239750-A-T
• rs12032329
• NM_004000.3:c.918+818A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004000.3(CHI3L2):​c.918+818A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0885 in 152,198 control chromosomes in the GnomAD database, including 941 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 0.089 (941 hom., cov: 32)
• Consequence: CHI3L2 NM_004000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHI3L2	NM_004000.3	c.918+818A>T		intron_variant	Intron 8 of 10	ENST00000369748.9	NP_003991.2
CHI3L2	NM_001025197.1	c.888+818A>T		intron_variant	Intron 7 of 9		NP_001020368.1
CHI3L2	NM_001025199.2	c.681+818A>T		intron_variant	Intron 7 of 9		NP_001020370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHI3L2	ENST00000369748.9	c.918+818A>T		intron_variant	Intron 8 of 10	1	NM_004000.3	ENSP00000358763.4

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13476 AN: 152080 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.0798

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0885 AC: 13472 AN: 152198 Hom.: 941 Cov.: 32 AF XY: 0.0957 AC XY: 7119 AN XY: 74402

African (AFR) AF: 0.0288 AC: 1195 AN: 41542

American (AMR) AF: 0.102 AC: 1555 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3468

East Asian (EAS) AF: 0.354 AC: 1831 AN: 5170

South Asian (SAS) AF: 0.185 AC: 889 AN: 4814

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10590

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5764 AN: 68002

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0736 Hom.: 55

Bravo AF: 0.0802

Asia WGS AF: 0.219 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12032329; hg19: chr1-111782372;