1-203238392-T-C

Variant names:

• chr1-203238392-T-C
• rs2494287
• ENST00000484834.5:n.4382+2071A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484834.5(CHIT1):​n.4382+2071A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,170 control chromosomes in the GnomAD database, including 60,258 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 0.89 (60258 hom., cov: 31)
• Consequence: CHIT1 ENST00000484834.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 8 publications found

Genes affected

CHIT1 (HGNC:1936): (chitinase 1) Chitotriosidase is secreted by activated human macrophages and is markedly elevated in plasma of Gaucher disease patients. The expression of chitotriosidase occurs only at a late stage of differentiation of monocytes to activated macrophages in culture. Human macrophages can synthesize a functional chitotriosidase, a highly conserved enzyme with a strongly regulated expression. This enzyme may play a role in the degradation of chitin-containing pathogens. Several alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484834.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHIT1	ENST00000484834.5	TSL:2	n.4382+2071A>G		intron	N/A
	CHIT1	ENST00000513472.5	TSL:3	n.151+2071A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134932 AN: 152052 Hom.: 60216 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.891

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.887 AC: 135026 AN: 152170 Hom.: 60258 Cov.: 31 AF XY: 0.885 AC XY: 65866 AN XY: 74384

African (AFR) AF: 0.940 AC: 39015 AN: 41520

American (AMR) AF: 0.762 AC: 11636 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3259 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3736 AN: 5142

South Asian (SAS) AF: 0.824 AC: 3981 AN: 4830

European-Finnish (FIN) AF: 0.946 AC: 10027 AN: 10594

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60406 AN: 68026

Other (OTH) AF: 0.894 AC: 1884 AN: 2108

Alfa AF: 0.882 Hom.: 256155

Bravo AF: 0.873

Asia WGS AF: 0.801 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2494287; hg19: chr1-203207520;