Genetic Variant ENSG00000229283:n.149-2757G>A (chr1-111320684-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000426321.1(ENSG00000229283):n.149-2757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 570,792 control chromosomes in the GnomAD database, including 6,079 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 0.16 ( 2765 hom., cov: 32)

Exomes 𝑓: 0.12 ( 3314 hom. )

Consequence

ENSG00000229283
ENST00000426321.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Variant links:

Genes affected

ENSG00000229283 (HGNC:):

ENSG00000229283 links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIA	NM_201653.4 link	c.*218C>T		downstream_gene_variant		ENST00000369740.6	NP_970615.2	Q9BZP6-1A8K3T7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6 link	c.*218C>T		downstream_gene_variant		1	NM_201653.4	ENSP00000358755.1		Q9BZP6-1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24938

AN:

151896

Hom.:

2761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.0985

Gnomad ASJ

AF:

0.0812

Gnomad EAS

AF:

0.0955

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.0699

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.136

GnomAD4 exome

AF:

0.116

AC:

48732

AN:

418778

Hom.:

3314

AF XY:

0.118

AC XY:

25793

AN XY:

218952

show subpopulations

Gnomad4 AFR exome

AF:

0.322

Gnomad4 AMR exome

AF:

0.0771

Gnomad4 ASJ exome

AF:

0.0805

Gnomad4 EAS exome

AF:

0.0835

Gnomad4 SAS exome

AF:

0.157

Gnomad4 FIN exome

AF:

0.0839

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.117

GnomAD4 genome

AF:

0.164

AC:

24973

AN:

152014

Hom.:

2765

Cov.:

AF XY:

0.162

AC XY:

12076

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.319

Gnomad4 AMR

AF:

0.0981

Gnomad4 ASJ

AF:

0.0812

Gnomad4 EAS

AF:

0.0957

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.0699

Gnomad4 NFE

AF:

0.112

Gnomad4 OTH

AF:

0.136

Alfa

AF:

0.127

Hom.:

721

Bravo

AF:

0.169

Asia WGS

AF:

0.128

AC:

448

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

0.64

DANN

Benign

0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over