rs12127313
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
NM_201653.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0470
Publications
5 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]
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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.106 AC: 16154AN: 151986Hom.: 1083 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
16154
AN:
151986
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.106 AC: 16154AN: 152106Hom.: 1082 Cov.: 32 AF XY: 0.105 AC XY: 7801AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
16154
AN:
152106
Hom.:
Cov.:
32
AF XY:
AC XY:
7801
AN XY:
74344
show subpopulations
African (AFR)
AF:
AC:
1668
AN:
41508
American (AMR)
AF:
AC:
1308
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
307
AN:
3470
East Asian (EAS)
AF:
AC:
60
AN:
5178
South Asian (SAS)
AF:
AC:
455
AN:
4818
European-Finnish (FIN)
AF:
AC:
1621
AN:
10568
Middle Eastern (MID)
AF:
AC:
37
AN:
294
European-Non Finnish (NFE)
AF:
AC:
10351
AN:
67988
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.