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rs1800871

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_153758.5(IL19):c.-149+2211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,064 control chromosomes in the GnomAD database, including 36,734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (‚ėÖ).

Frequency

Genomes: ūĚĎď 0.69 ( 36734 hom., cov: 31)

Consequence

IL19
NM_153758.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: -0.292
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 1-206773289-A-G is Benign according to our data. Variant chr1-206773289-A-G is described in ClinVar as [Benign]. Clinvar id is 1166836.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL19NM_153758.5 linkuse as main transcriptc.-149+2211A>G intron_variant ENST00000659997.3
IL19NM_001393490.1 linkuse as main transcriptc.-149+2459A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL19ENST00000659997.3 linkuse as main transcriptc.-149+2211A>G intron_variant NM_153758.5 P1Q9UHD0-1

Frequencies

GnomAD3 genomes
AF:
0.687
AC:
104313
AN:
151946
Hom.:
36709
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.589
Gnomad AMI
AF:
0.707
Gnomad AMR
AF:
0.674
Gnomad ASJ
AF:
0.750
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.564
Gnomad FIN
AF:
0.776
Gnomad MID
AF:
0.688
Gnomad NFE
AF:
0.768
Gnomad OTH
AF:
0.679
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.687
AC:
104398
AN:
152064
Hom.:
36734
Cov.:
31
AF XY:
0.683
AC XY:
50744
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.589
Gnomad4 AMR
AF:
0.674
Gnomad4 ASJ
AF:
0.750
Gnomad4 EAS
AF:
0.315
Gnomad4 SAS
AF:
0.564
Gnomad4 FIN
AF:
0.776
Gnomad4 NFE
AF:
0.768
Gnomad4 OTH
AF:
0.681
Alfa
AF:
0.737
Hom.:
80969
Bravo
AF:
0.674
Asia WGS
AF:
0.488
AC:
1703
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inflammatory bowel disease Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 19, 2024- -
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
-0.93
Cadd
Benign
1.1
Dann
Benign
0.32

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: rs1800871; hg19: chr1-206946634; API