chr1-111314863-A-C

Variant names:

• chr1-111314863-A-C
• rs2820072
• NM_201653.4:c.314+267A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.81).
• 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 rank	MANE	Protein	UniProt
CHIA	NM_201653.4	c.314+267A>C		intron_variant	Intron 5 of 11	ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.314+267A>C		intron_variant	Intron 5 of 11	1	NM_201653.4	ENSP00000358755.1

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

African (AFR) AF: 0.582 AC: 5010 AN: 8602

American (AMR) AF: 0.333 AC: 3664 AN: 11006

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 5402 AN: 10436

East Asian (EAS) AF: 0.445 AC: 9505 AN: 21362

South Asian (SAS) AF: 0.656 AC: 17299 AN: 26364

European-Finnish (FIN) AF: 0.564 AC: 11102 AN: 19688

Middle Eastern (MID) AF: 0.599 AC: 930 AN: 1552

European-Non Finnish (NFE) AF: 0.579 AC: 111757 AN: 192864

Other (OTH) AF: 0.549 AC: 10404 AN: 18944

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

African (AFR) AF: 0.578 AC: 23965 AN: 41482

American (AMR) AF: 0.391 AC: 5976 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1776 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2341 AN: 5168

South Asian (SAS) AF: 0.651 AC: 3137 AN: 4820

European-Finnish (FIN) AF: 0.569 AC: 6008 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39747 AN: 67990

Other (OTH) AF: 0.518 AC: 1095 AN: 2112

Alfa AF: 0.557 Hom.: 31525

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
PhyloP100		0.50
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: rs2820072; hg19: chr1-111857485;