chr1-111230823-T-A

Variant names:

• chr1-111230823-T-A
• rs538439659
• ENST00000466741:c.-86T>A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001025199.2(CHI3L2):​c.-86T>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: CHI3L2 NM_001025199.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.98

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHI3L2	NM_004000.3	c.152T>A	p.Ile51Asn	missense_variant	Exon 3 of 11	ENST00000369748.9	NP_003991.2
CHI3L2	NM_001025199.2	c.-86T>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 10		NP_001020370.1
CHI3L2	NM_001025197.1	c.122T>A	p.Ile41Asn	missense_variant	Exon 2 of 10		NP_001020368.1
CHI3L2	NM_001025199.2	c.-86T>A		5_prime_UTR_variant	Exon 2 of 10		NP_001020370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHI3L2	ENST00000369748.9	c.152T>A	p.Ile51Asn	missense_variant	Exon 3 of 11	1	NM_004000.3	ENSP00000358763.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.69
BayesDel_addAF	Benign	-0.071	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.21	T;.;T;.;T;T
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.47
FATHMM_MKL	Benign	0.15	N
LIST_S2	Uncertain	0.93	.;D;D;D;D;D
M_CAP	Benign	0.015	T
MetaRNN	Uncertain	0.66	D;D;D;D;D;D
MetaSVM	Benign	-0.71	T
MutationAssessor	Pathogenic	4.1	H;.;.;.;H;.
PrimateAI	Benign	0.24	T
PROVEAN	Pathogenic	-5.8	D;D;D;D;D;D
REVEL	Benign	0.10
Sift	Pathogenic	0.0	D;D;D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D;D;D
Polyphen		0.98	D;.;.;.;D;.
Vest4		0.43
MutPred		0.83		Gain of disorder (P = 0.0061);Gain of disorder (P = 0.0061);Gain of disorder (P = 0.0061);.;Gain of disorder (P = 0.0061);Gain of disorder (P = 0.0061);
MVP		0.16
MPC		0.10
ClinPred		0.98	D
GERP RS		-1.1
Varity_R		0.93
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs538439659; hg19: chr1-111773445;