rs12127313

Variant names:

• chr1-111311498-G-A
• rs12127313
• NM_201653.4:c.26-191G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-111311498-G-A
• chr1-111311498-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.26-191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,106 control chromosomes in the GnomAD database, including 1,082 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 0.11 (1082 hom., cov: 32)
• Consequence: CHIA NM_201653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIA	NM_201653.4	c.26-191G>A		intron_variant	Intron 2 of 11	ENST00000369740.6	NP_970615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIA	ENST00000369740.6	c.26-191G>A		intron_variant	Intron 2 of 11	1	NM_201653.4	ENSP00000358755.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16154 AN: 151986 Hom.: 1083 Cov.: 32

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.113

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.106 AC: 16154 AN: 152106 Hom.: 1082 Cov.: 32 AF XY: 0.105 AC XY: 7801 AN XY: 74344

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.114

Alfa AF: 0.132 Hom.: 1930

Bravo AF: 0.0961

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.65

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: rs12127313; hg19: chr1-111854120;