1-111320684-C-T

Variant names:

• chr1-111320684-C-T
• rs2820093
• ENST00000426321.2:n.392-2757G>A

Variant summary

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

The ENST00000426321.2(ENSG00000229283):​n.392-2757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 570,792 control chromosomes in the GnomAD database, including 6,079 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 0.16 (2765 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3314 hom.)
• Consequence: ENSG00000229283 ENST00000426321.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 7 publications found

Genes affected

ENSG00000229283 (HGNC:):

CHIA (HGNC:17432): (chitinase acidic) The protein encoded by this gene degrades chitin, which is found in the cell wall of most fungi as well as in arthropods and some nematodes. The encoded protein can also stimulate interleukin 13 expression, and variations in this gene can lead to asthma susceptibility. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIA	NM_201653.4	c.*218C>T		downstream_gene_variant		ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.*218C>T		downstream_gene_variant		1	NM_201653.4	ENSP00000358755.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24938 AN: 151896 Hom.: 2761 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.116 AC: 48732 AN: 418778 Hom.: 3314 AF XY: 0.118 AC XY: 25793 AN XY: 218952

African (AFR) AF: 0.322 AC: 3859 AN: 11988

American (AMR) AF: 0.0771 AC: 1381 AN: 17914

Ashkenazi Jewish (ASJ) AF: 0.0805 AC: 1052 AN: 13062

East Asian (EAS) AF: 0.0835 AC: 2462 AN: 29488

South Asian (SAS) AF: 0.157 AC: 6432 AN: 41008

European-Finnish (FIN) AF: 0.0839 AC: 2310 AN: 27530

Middle Eastern (MID) AF: 0.108 AC: 202 AN: 1868

European-Non Finnish (NFE) AF: 0.112 AC: 28148 AN: 251342

Other (OTH) AF: 0.117 AC: 2886 AN: 24578

GnomAD4 genome AF: 0.164 AC: 24973 AN: 152014 Hom.: 2765 Cov.: 32 AF XY: 0.162 AC XY: 12076 AN XY: 74338

African (AFR) AF: 0.319 AC: 13218 AN: 41410

American (AMR) AF: 0.0981 AC: 1500 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0812 AC: 282 AN: 3472

East Asian (EAS) AF: 0.0957 AC: 495 AN: 5170

South Asian (SAS) AF: 0.157 AC: 754 AN: 4812

European-Finnish (FIN) AF: 0.0699 AC: 741 AN: 10606

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7615 AN: 67938

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.126 Hom.: 778

Bravo AF: 0.169

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2820093; hg19: chr1-111863306; COSMIC: COSV107430161;