rs11584291

Variant names:

• chr1-111304181-C-T
• rs11584291
• NM_201653.4:c.-68-6219C>T

Variant summary

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

The NM_201653.4(CHIA):​c.-68-6219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,922 control chromosomes in the GnomAD database, including 6,173 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 0.28 (6173 hom., cov: 32)
• Consequence: CHIA NM_201653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 12 publications found

Genes affected

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIA	NM_201653.4	c.-68-6219C>T		intron_variant	Intron 1 of 11	ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.-68-6219C>T		intron_variant	Intron 1 of 11	1	NM_201653.4	ENSP00000358755.1
CHIA	ENST00000422815.5	c.90-10359C>T		intron_variant	Intron 1 of 8	1		ENSP00000387671.1
CHIA	ENST00000483391.5	c.-60-10359C>T		intron_variant	Intron 1 of 7	1		ENSP00000436946.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42299 AN: 151804 Hom.: 6177 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.279 AC: 42322 AN: 151922 Hom.: 6173 Cov.: 32 AF XY: 0.276 AC XY: 20490 AN XY: 74248

African (AFR) AF: 0.202 AC: 8392 AN: 41466

American (AMR) AF: 0.324 AC: 4950 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1843 AN: 5178

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2780 AN: 10506

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21062 AN: 67894

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.301 Hom.: 3676

Bravo AF: 0.283

Asia WGS AF: 0.280 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs11584291; hg19: chr1-111846803;