NM_153758.5:c.-3+10579A>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_153758.5(IL19):c.-3+10579A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,044 control chromosomes in the GnomAD database, including 7,659 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 0.31 ( 7659 hom., cov: 32)
Consequence
IL19
NM_153758.5 intron
NM_153758.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0470
Publications
6 publications found
Genes affected
IL19 (HGNC:5990): (interleukin 19) The protein encoded by this gene is a cytokine that belongs to the IL10 cytokine subfamily. This cytokine is found to be preferentially expressed in monocytes. It can bind the IL20 receptor complex and lead to the activation of the signal transducer and activator of transcription 3 (STAT3). A similar cytokine in mouse is reported to up-regulate the expression of IL6 and TNF-alpha and induce apoptosis, which suggests a role of this cytokine in inflammatory responses. Alternatively spliced transcript variants encoding the distinct isoforms have been described. [provided by RefSeq, Jul 2008]
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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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL19 | ENST00000659997.3 | c.-3+10579A>T | intron_variant | Intron 2 of 6 | NM_153758.5 | ENSP00000499459.2 | ||||
IL19 | ENST00000656872.2 | c.-3+10579A>T | intron_variant | Intron 2 of 6 | ENSP00000499487.2 | |||||
IL19 | ENST00000662320.1 | n.213+10579A>T | intron_variant | Intron 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.310 AC: 47137AN: 151926Hom.: 7651 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
47137
AN:
151926
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: 0.310 AC: 47181AN: 152044Hom.: 7659 Cov.: 32 AF XY: 0.306 AC XY: 22724AN XY: 74320 show subpopulations
GnomAD4 genome
AF:
AC:
47181
AN:
152044
Hom.:
Cov.:
32
AF XY:
AC XY:
22724
AN XY:
74320
show subpopulations
African (AFR)
AF:
AC:
15638
AN:
41456
American (AMR)
AF:
AC:
3909
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
600
AN:
3470
East Asian (EAS)
AF:
AC:
2129
AN:
5162
South Asian (SAS)
AF:
AC:
870
AN:
4822
European-Finnish (FIN)
AF:
AC:
3048
AN:
10570
Middle Eastern (MID)
AF:
AC:
55
AN:
294
European-Non Finnish (NFE)
AF:
AC:
20074
AN:
67972
Other (OTH)
AF:
AC:
588
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1652
3304
4956
6608
8260
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
466
932
1398
1864
2330
<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:
Asia WGS
AF:
AC:
1029
AN:
3478
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
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