rs1077059

Positions:

• chr1-111242473-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004000.3(CHI3L2):​c.*2+107C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 1,234,760 control chromosomes in the GnomAD database, including 1,436 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 0.065 (723 hom., cov: 32)
  • Exomes 𝑓: 0.026 (713 hom.)
• Consequence: CHI3L2 NM_004000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHI3L2	NM_004000.3	c.*2+107C>G		intron_variant		ENST00000369748.9
CHI3L2	NM_001025197.1	c.*2+107C>G		intron_variant
CHI3L2	NM_001025199.2	c.*2+107C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHI3L2	ENST00000369748.9	c.*2+107C>G		intron_variant		1	NM_004000.3	P1

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9872 AN: 152054 Hom.: 723 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00973

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0468

GnomAD4 exome AF: 0.0256 AC: 27677 AN: 1082588 Hom.: 713 Cov.: 14 AF XY: 0.0249 AC XY: 13270 AN XY: 532528

Gnomad4 AFR exome AF: 0.178

Gnomad4 AMR exome AF: 0.0341

Gnomad4 ASJ exome AF: 0.00592

Gnomad4 EAS exome AF: 0.000118

Gnomad4 SAS exome AF: 0.0110

Gnomad4 FIN exome AF: 0.0466

Gnomad4 NFE exome AF: 0.0220

Gnomad4 OTH exome AF: 0.0312

GnomAD4 genome AF: 0.0649 AC: 9881 AN: 152172 Hom.: 723 Cov.: 32 AF XY: 0.0642 AC XY: 4772 AN XY: 74374

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00953

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0209

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0449 Hom.: 41

Bravo AF: 0.0700

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.0
DANN	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs1077059; hg19: chr1-111785095;