rs2820072

Positions:

• chr1-111314863-A-C

Variant summary

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

The NM_201653.4(CHIA):​c.314+267A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 462,896 control chromosomes in the GnomAD database, including 74,303 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 0.56 (23923 hom., cov: 31)
  • Exomes 𝑓: 0.56 (50380 hom.)
• Consequence: CHIA NM_201653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHIA	NM_201653.4	c.314+267A>C		intron_variant		ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.314+267A>C		intron_variant		1	NM_201653.4	ENSP00000358755	P1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84641 AN: 151960 Hom.: 23909 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.563 AC: 175073 AN: 310818 Hom.: 50380 Cov.: 2 AF XY: 0.568 AC XY: 91978 AN XY: 161986

Gnomad4 AFR exome AF: 0.582

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.518

Gnomad4 EAS exome AF: 0.445

Gnomad4 SAS exome AF: 0.656

Gnomad4 FIN exome AF: 0.564

Gnomad4 NFE exome AF: 0.579

Gnomad4 OTH exome AF: 0.549

GnomAD4 genome AF: 0.557 AC: 84706 AN: 152078 Hom.: 23923 Cov.: 31 AF XY: 0.556 AC XY: 41348 AN XY: 74328

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.518

Alfa AF: 0.561 Hom.: 24405

Bravo AF: 0.534

Asia WGS AF: 0.522 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	16
DANN	Benign	0.87

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: rs2820072; hg19: chr1-111857485;