1-111229743-G-C

Variant names:

• chr1-111229743-G-C
• rs12070867
• ENST00000466741.5:c.-306G>C

Variant summary

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

The NM_001025199.2(CHI3L2):​c.-306G>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000788 in 1,269,012 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: 29)
  • Exomes 𝑓: 7.9e-7 (0 hom.)
• Consequence: CHI3L2 NM_001025199.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 3 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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025199.2. 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.41-109G>C		intron	N/A	NP_003991.2	Q15782-4
	CHI3L2	NM_001025199.2		c.-306G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 10	NP_001020370.1	Q15782-5
	CHI3L2	NM_001025199.2		c.-306G>C		5_prime_UTR	Exon 1 of 10	NP_001020370.1	Q15782-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHI3L2	ENST00000466741.5	TSL:1	c.-306G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 10	ENSP00000437086.1	Q15782-5
	CHI3L2	ENST00000466741.5	TSL:1	c.-306G>C		5_prime_UTR	Exon 1 of 10	ENSP00000437086.1	Q15782-5
	CHI3L2	ENST00000369748.9	TSL:1 MANE Select	c.41-109G>C		intron	N/A	ENSP00000358763.4	Q15782-4

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 7.88e-7 AC: 1 AN: 1269012 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 626800

African (AFR) AF: 0.00 AC: 0 AN: 26926

American (AMR) AF: 0.00 AC: 0 AN: 31756

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20072

East Asian (EAS) AF: 0.00 AC: 0 AN: 32916

South Asian (SAS) AF: 0.00 AC: 0 AN: 69974

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45750

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4638

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 986836

Other (OTH) AF: 0.0000199 AC: 1 AN: 50144

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.76
PhyloP100		-0.28
PromoterAI		-0.0038	Neutral

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: rs12070867; hg19: chr1-111772365;