1-111317216-T-G

Position:

• chr1-111317216-T-G

Variant summary

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

The NM_201653.4(CHIA):​c.481-465T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 167,524 control chromosomes in the GnomAD database, including 6,026 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 0.25 (5452 hom., cov: 32)
  • Exomes 𝑓: 0.25 (574 hom.)
• Consequence: CHIA NM_201653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHIA	NM_201653.4	c.481-465T>G		intron_variant		ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.481-465T>G		intron_variant		1	NM_201653.4	ENSP00000358755.1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38110 AN: 151994 Hom.: 5455 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.250 AC: 3854 AN: 15412 Hom.: 574 Cov.: 0 AF XY: 0.253 AC XY: 2068 AN XY: 8172

Gnomad4 AFR exome AF: 0.0867

Gnomad4 AMR exome AF: 0.165

Gnomad4 ASJ exome AF: 0.262

Gnomad4 EAS exome AF: 0.274

Gnomad4 SAS exome AF: 0.351

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.266

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.250 AC: 38101 AN: 152112 Hom.: 5452 Cov.: 32 AF XY: 0.252 AC XY: 18767 AN XY: 74340

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.244

Alfa AF: 0.293 Hom.: 8826

Bravo AF: 0.231

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.47

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: rs12034576; hg19: chr1-111859838;