1-111317290-G-T

Position:

• chr1-111317290-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201653.4(CHIA):​c.481-391G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 180,872 control chromosomes in the GnomAD database, including 13,603 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 0.36 (11120 hom., cov: 31)
  • Exomes 𝑓: 0.39 (2483 hom.)
• Consequence: CHIA NM_201653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

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]

CHIA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHIA	NM_201653.4	c.481-391G>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.481-391G>T		intron_variant		1	NM_201653.4	ENSP00000358755.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54664 AN: 151826 Hom.: 11124 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.387 AC: 11205 AN: 28928 Hom.: 2483 Cov.: 0 AF XY: 0.387 AC XY: 5878 AN XY: 15206

Gnomad4 AFR exome AF: 0.139

Gnomad4 AMR exome AF: 0.245

Gnomad4 ASJ exome AF: 0.409

Gnomad4 EAS exome AF: 0.328

Gnomad4 SAS exome AF: 0.459

Gnomad4 FIN exome AF: 0.433

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.387

GnomAD4 genome AF: 0.360 AC: 54658 AN: 151944 Hom.: 11120 Cov.: 31 AF XY: 0.360 AC XY: 26747 AN XY: 74258

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.358

Alfa AF: 0.438 Hom.: 19767

Bravo AF: 0.330

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.66

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: rs10494134; hg19: chr1-111859912;