rs2484460

chr1-111220259-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445067.6(CHI3L2):c.-156-5685T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,138 control chromosomes in the GnomAD database, including 1,776 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 0.15 (1776 hom., cov: 31)
• Consequence: CHI3L2 ENST00000445067.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L2	ENST00000445067.6	c.-156-5685T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22127 AN: 152020 Hom.: 1773 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.146 AC: 22153 AN: 152138 Hom.: 1776 Cov.: 31 AF XY: 0.144 AC XY: 10722 AN XY: 74374

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.0966

Gnomad4 EAS AF: 0.0924

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0727

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.122

Alfa AF: 0.152 Hom.: 441

Bravo AF: 0.158

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.51

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

Other links and lift over

dbSNP: rs2484460; hg19: chr1-111762881;