rs12127313

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470

Publications

5 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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
CHIANM_201653.4 linkc.26-191G>A intron_variant Intron 2 of 11 ENST00000369740.6 NP_970615.2 Q9BZP6-1A8K3T7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHIAENST00000369740.6 linkc.26-191G>A intron_variant Intron 2 of 11 1 NM_201653.4 ENSP00000358755.1 Q9BZP6-1

Frequencies

GnomAD3 genomes
AF:
0.106
AC:
16154
AN:
151986
Hom.:
1083
Cov.:
32
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.0402
AC:
1668
AN:
41508
American (AMR)
AF:
0.0856
AC:
1308
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.0885
AC:
307
AN:
3470
East Asian (EAS)
AF:
0.0116
AC:
60
AN:
5178
South Asian (SAS)
AF:
0.0944
AC:
455
AN:
4818
European-Finnish (FIN)
AF:
0.153
AC:
1621
AN:
10568
Middle Eastern (MID)
AF:
0.126
AC:
37
AN:
294
European-Non Finnish (NFE)
AF:
0.152
AC:
10351
AN:
67988
Other (OTH)
AF:
0.114
AC:
239
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
722
1444
2167
2889
3611
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
188
376
564
752
940
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.129
Hom.:
2362
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
PhyloP100
-0.047
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

Publications

Other links and lift over

dbSNP: rs12127313; hg19: chr1-111854120; API