rs2484460

Variant names:

• chr1-111220259-T-C
• rs2484460
• ENST00000445067.6:c.-156-5685T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHI3L2	ENST00000445067.6	c.-156-5685T>C		intron_variant	Intron 1 of 12	5		ENSP00000437082.1

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

African (AFR) AF: 0.172 AC: 7145 AN: 41474

American (AMR) AF: 0.216 AC: 3294 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0966 AC: 335 AN: 3468

East Asian (EAS) AF: 0.0924 AC: 479 AN: 5182

South Asian (SAS) AF: 0.129 AC: 620 AN: 4812

European-Finnish (FIN) AF: 0.0727 AC: 772 AN: 10620

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9062 AN: 68006

Other (OTH) AF: 0.122 AC: 256 AN: 2100

Alfa AF: 0.149 Hom.: 682

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
PhyloP100		-0.27
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: rs2484460; hg19: chr1-111762881;