1-111294513-C-T

Variant names:

• chr1-111294513-C-T
• rs7411387
• NM_201653.4:c.-69+3563C>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.-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
• 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=-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 rank	MANE	Protein	UniProt
CHIA	NM_201653.4	c.-69+3563C>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.-69+3563C>T		intron_variant	Intron 1 of 11	1	NM_201653.4	ENSP00000358755.1
CHIA	ENST00000422815.5	c.89+3563C>T		intron_variant	Intron 1 of 8	1		ENSP00000387671.1
CHIA	ENST00000483391.5	c.-61+3563C>T		intron_variant	Intron 1 of 7	1		ENSP00000436946.1

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

African (AFR) AF: 0.679 AC: 28114 AN: 41410

American (AMR) AF: 0.556 AC: 8498 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2346 AN: 3464

East Asian (EAS) AF: 0.633 AC: 3271 AN: 5166

South Asian (SAS) AF: 0.620 AC: 2988 AN: 4820

European-Finnish (FIN) AF: 0.609 AC: 6412 AN: 10530

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.615 AC: 41794 AN: 67908

Other (OTH) AF: 0.615 AC: 1295 AN: 2106

Alfa AF: 0.616 Hom.: 32913

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
PhyloP100		-0.63
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: rs7411387; hg19: chr1-111837135;