NM_153758.5:c.-3+10579A>T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470

Publications

6 publications found
Variant links:
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]

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL19NM_153758.5 linkc.-3+10579A>T intron_variant Intron 2 of 6 ENST00000659997.3 NP_715639.2 Q9UHD0-1
IL19NM_001393490.1 linkc.-3+10579A>T intron_variant Intron 2 of 6 NP_001380419.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL19ENST00000659997.3 linkc.-3+10579A>T intron_variant Intron 2 of 6 NM_153758.5 ENSP00000499459.2 Q9UHD0-1
IL19ENST00000656872.2 linkc.-3+10579A>T intron_variant Intron 2 of 6 ENSP00000499487.2 Q9UHD0-1
IL19ENST00000662320.1 linkn.213+10579A>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.310
AC:
47137
AN:
151926
Hom.:
7651
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.377
Gnomad AMI
AF:
0.296
Gnomad AMR
AF:
0.255
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.413
Gnomad SAS
AF:
0.181
Gnomad FIN
AF:
0.288
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.281
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.310
AC:
47181
AN:
152044
Hom.:
7659
Cov.:
32
AF XY:
0.306
AC XY:
22724
AN XY:
74320
show subpopulations
African (AFR)
AF:
0.377
AC:
15638
AN:
41456
American (AMR)
AF:
0.256
AC:
3909
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.173
AC:
600
AN:
3470
East Asian (EAS)
AF:
0.412
AC:
2129
AN:
5162
South Asian (SAS)
AF:
0.180
AC:
870
AN:
4822
European-Finnish (FIN)
AF:
0.288
AC:
3048
AN:
10570
Middle Eastern (MID)
AF:
0.187
AC:
55
AN:
294
European-Non Finnish (NFE)
AF:
0.295
AC:
20074
AN:
67972
Other (OTH)
AF:
0.279
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:
0.187
Hom.:
367
Bravo
AF:
0.312
Asia WGS
AF:
0.296
AC:
1029
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.6
DANN
Benign
0.76
PhyloP100
-0.047
Mutation Taster
=99/1
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: rs12409577; hg19: chr1-206982930; API