rs942693

Variant names:

• chr1-111241536-T-A
• rs942693
• NM_004000.3:c.1035+93T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-111241536-T-A
• chr1-111241536-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004000.3(CHI3L2):​c.1035+93T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CHI3L2 NM_004000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004000.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHI3L2	NM_004000.3	MANE Select	c.1035+93T>A		intron	N/A	NP_003991.2	Q15782-4
	CHI3L2	NM_001025197.1		c.1005+93T>A		intron	N/A	NP_001020368.1	Q15782-6
	CHI3L2	NM_001025199.2		c.798+93T>A		intron	N/A	NP_001020370.1	Q15782-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHI3L2	ENST00000369748.9	TSL:1 MANE Select	c.1035+93T>A		intron	N/A	ENSP00000358763.4	Q15782-4
	CHI3L2	ENST00000466741.5	TSL:1	c.798+93T>A		intron	N/A	ENSP00000437086.1	Q15782-5
	CHI3L2	ENST00000445067.6	TSL:5	c.1035+93T>A		intron	N/A	ENSP00000437082.1	Q15782-4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 562656 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 298508

African (AFR) AF: 0.00 AC: 0 AN: 15498

American (AMR) AF: 0.00 AC: 0 AN: 27578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15150

East Asian (EAS) AF: 0.00 AC: 0 AN: 34502

South Asian (SAS) AF: 0.00 AC: 0 AN: 52442

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47072

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3702

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 336834

Other (OTH) AF: 0.00 AC: 0 AN: 29878

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 11253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.78
PhyloP100		0.088

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs942693; hg19: chr1-111784158;