1-111294513-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.-69+3563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,882 control chromosomes in the GnomAD database, including 30,189 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 0.63 (30189 hom., cov: 31)
• Consequence: CHIA NM_201653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHIA	NM_201653.4	c.-69+3563C>T		intron_variant		ENST00000369740.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHIA	ENST00000369740.6	c.-69+3563C>T		intron_variant		1	NM_201653.4	P1
CHIA	ENST00000422815.5	c.89+3563C>T		intron_variant		1
CHIA	ENST00000483391.5	c.-61+3563C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95319 AN: 151764 Hom.: 30169 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.628 AC: 95386 AN: 151882 Hom.: 30189 Cov.: 31 AF XY: 0.626 AC XY: 46486 AN XY: 74230

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.615

Alfa AF: 0.612 Hom.: 20013

Bravo AF: 0.623

Asia WGS AF: 0.631 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.72
Dann	Benign	0.35

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: rs7411387; hg19: chr1-111837135;