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rs1800896

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153758.5(IL19):c.-149+2474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,018 control chromosomes in the GnomAD database, including 12,917 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).

Frequency

Genomes: ūĚĎď 0.40 ( 12917 hom., cov: 29)

Consequence

IL19
NM_153758.5 intron

Scores

2

Clinical Significance

Uncertain risk allele no assertion criteria provided O:1

Conservation

PhyloP100: 0.0260
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]
IL10 (HGNC:5962): (interleukin 10) The protein encoded by this gene is a cytokine produced primarily by monocytes and to a lesser extent by lymphocytes. This cytokine has pleiotropic effects in immunoregulation and inflammation. It down-regulates the expression of Th1 cytokines, MHC class II Ags, and costimulatory molecules on macrophages. It also enhances B cell survival, proliferation, and antibody production. This cytokine can block NF-kappa B activity, and is involved in the regulation of the JAK-STAT signaling pathway. Knockout studies in mice suggested the function of this cytokine as an essential immunoregulator in the intestinal tract. Mutations in this gene are associated with an increased susceptibility to HIV-1 infection and rheumatoid arthritis. [provided by RefSeq, May 2020]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL19NM_153758.5 linkuse as main transcriptc.-149+2474T>C intron_variant ENST00000659997.3
IL19NM_001393490.1 linkuse as main transcriptc.-149+2722T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL19ENST00000659997.3 linkuse as main transcriptc.-149+2474T>C intron_variant NM_153758.5 P1Q9UHD0-1

Frequencies

GnomAD3 genomes
AF:
0.401
AC:
60462
AN:
150900
Hom.:
12903
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.337
Gnomad AMI
AF:
0.443
Gnomad AMR
AF:
0.303
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.0529
Gnomad SAS
AF:
0.250
Gnomad FIN
AF:
0.475
Gnomad MID
AF:
0.347
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.382
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
60505
AN:
151018
Hom.:
12917
Cov.:
29
AF XY:
0.393
AC XY:
28989
AN XY:
73686
show subpopulations
Gnomad4 AFR
AF:
0.337
Gnomad4 AMR
AF:
0.302
Gnomad4 ASJ
AF:
0.408
Gnomad4 EAS
AF:
0.0528
Gnomad4 SAS
AF:
0.249
Gnomad4 FIN
AF:
0.475
Gnomad4 NFE
AF:
0.487
Gnomad4 OTH
AF:
0.378
Alfa
AF:
0.453
Hom.:
32372
Bravo
AF:
0.387
Asia WGS
AF:
0.159
AC:
554
AN:
3478

ClinVar

Significance: Uncertain risk allele
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Leprosy, susceptibility to, 1 Other:1
Uncertain risk allele, no assertion criteria providedcase-controlCentro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras AcostaJun 10, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
5.3
Dann
Benign
0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1800896; hg19: chr1-206946897; API