rs17351243

Variant names:

• chr1-206786182-G-A
• rs17351243
• NM_153758.5:c.-148-12679G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-206786182-G-A
• chr1-206786182-G-C
• chr1-206786182-G-T

Variant summary

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

The NM_153758.5(IL19):​c.-148-12679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,980 control chromosomes in the GnomAD database, including 13,162 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 0.38 (13162 hom., cov: 31)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 15 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.-148-12679G>A		intron_variant	Intron 1 of 6	ENST00000659997.3	NP_715639.2
IL19	NM_001393490.1	c.-148-12679G>A		intron_variant	Intron 1 of 6		NP_001380419.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000659997.3	c.-148-12679G>A		intron_variant	Intron 1 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000656872.2	c.-148-12679G>A		intron_variant	Intron 1 of 6			ENSP00000499487.2
IL19	ENST00000662320.1	n.68-12679G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57690 AN: 151862 Hom.: 13167 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.380 AC: 57681 AN: 151980 Hom.: 13162 Cov.: 31 AF XY: 0.383 AC XY: 28466 AN XY: 74280

African (AFR) AF: 0.119 AC: 4917 AN: 41424

American (AMR) AF: 0.474 AC: 7243 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1976 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3555 AN: 5172

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4637 AN: 10550

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31886 AN: 67954

Other (OTH) AF: 0.428 AC: 905 AN: 2114

Alfa AF: 0.413 Hom.: 15310

Bravo AF: 0.372

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.27
DANN	Benign	0.70
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs17351243; hg19: chr1-206959527;