rs1056825

Variant names:

• chr1-111243308-T-A
• rs1056825
• NM_004000.3:c.*94T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-111243308-T-A
• chr1-111243308-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.*94T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 301,660 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000033 (0 hom.)
• Consequence: CHI3L2 NM_004000.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 7 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=-0.86).

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.*94T>A		3_prime_UTR	Exon 11 of 11	NP_003991.2	Q15782-4
	CHI3L2	NM_001025197.1		c.*94T>A		3_prime_UTR	Exon 10 of 10	NP_001020368.1	Q15782-6
	CHI3L2	NM_001025199.2		c.*94T>A		3_prime_UTR	Exon 10 of 10	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.*94T>A		3_prime_UTR	Exon 11 of 11	ENSP00000358763.4	Q15782-4
	CHI3L2	ENST00000466741.5	TSL:1	c.*94T>A		3_prime_UTR	Exon 10 of 10	ENSP00000437086.1	Q15782-5
	CHI3L2	ENST00000445067.6	TSL:5	c.*94T>A		3_prime_UTR	Exon 13 of 13	ENSP00000437082.1	Q15782-4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000331 AC: 1 AN: 301660 Hom.: 0 Cov.: 0 AF XY: 0.00000583 AC XY: 1 AN XY: 171636

African (AFR) AF: 0.00 AC: 0 AN: 8550

American (AMR) AF: 0.00 AC: 0 AN: 27138

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10674

East Asian (EAS) AF: 0.00 AC: 0 AN: 9180

South Asian (SAS) AF: 0.00 AC: 0 AN: 59598

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12326

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2596

European-Non Finnish (NFE) AF: 0.00000635 AC: 1 AN: 157492

Other (OTH) AF: 0.00 AC: 0 AN: 14106

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.73
PhyloP100		0.35

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: rs1056825; hg19: chr1-111785930;