rs11584291

Positions:

• chr1-111304181-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CHIA	NM_201653.4	c.-68-6219C>T		intron_variant		ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.-68-6219C>T		intron_variant		1	NM_201653.4	ENSP00000358755.1
CHIA	ENST00000422815.5	c.90-10359C>T		intron_variant		1		ENSP00000387671.1
CHIA	ENST00000483391.5	c.-60-10359C>T		intron_variant		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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.305

Alfa AF: 0.300 Hom.: 3300

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

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: rs11584291; hg19: chr1-111846803;