ENST00000479483.1:n.283+1979A>G

Variant names:

• chr1-203215760-T-C
• rs1417149
• ENST00000479483.1:n.283+1979A>G

Variant summary

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

The ENST00000479483.1(CHIT1):​n.283+1979A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,976 control chromosomes in the GnomAD database, including 19,494 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 0.49 (19494 hom., cov: 32)
• Consequence: CHIT1 ENST00000479483.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIT1	ENST00000479483.1	n.283+1979A>G		intron_variant	Intron 1 of 1	3
CHIT1	ENST00000484834.5	n.5388+1979A>G		intron_variant	Intron 11 of 11	2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74703 AN: 151858 Hom.: 19474 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.492 AC: 74766 AN: 151976 Hom.: 19494 Cov.: 32 AF XY: 0.503 AC XY: 37355 AN XY: 74276

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.521

Alfa AF: 0.467 Hom.: 4762

Bravo AF: 0.494

Asia WGS AF: 0.807 AC: 2801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417149; hg19: chr1-203184888;