rs1800891

Variant names:

• chr1-206775221-T-C
• rs1800891
• NM_153758.5:c.-149+4143T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153758.5(IL19):​c.-149+4143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,026 control chromosomes in the GnomAD database, including 275 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 0.060 (275 hom., cov: 31)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153758.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	NM_153758.5	MANE Select	c.-149+4143T>C		intron	N/A	NP_715639.2
	IL19	NM_001393490.1		c.-149+4391T>C		intron	N/A	NP_001380419.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.-149+4143T>C		intron	N/A	ENSP00000499459.2
	IL19	ENST00000656872.2		c.-149+4391T>C		intron	N/A	ENSP00000499487.2
	IL19	ENST00000662320.1		n.67+4391T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9125 AN: 151908 Hom.: 272 Cov.: 31

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0675

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0601 AC: 9143 AN: 152026 Hom.: 275 Cov.: 31 AF XY: 0.0599 AC XY: 4453 AN XY: 74348

African (AFR) AF: 0.0713 AC: 2954 AN: 41436

American (AMR) AF: 0.0527 AC: 806 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0160 AC: 77 AN: 4816

European-Finnish (FIN) AF: 0.0629 AC: 665 AN: 10568

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4144 AN: 67954

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0581 Hom.: 39

Bravo AF: 0.0616

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
DANN	Benign	0.069
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1800891; hg19: chr1-206948566;