rs2243193

Variant names:

• chr1-206842880-A-G
• rs2243193
• NM_153758.5:c.*258A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-206842880-A-G
• chr1-206842880-A-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.*258A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 383,218 control chromosomes in the GnomAD database, including 94,916 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 0.68 (36574 hom., cov: 33)
  • Exomes 𝑓: 0.70 (58342 hom.)
• Consequence: IL19 NM_153758.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 23 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]

LOC105372878 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 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.*258A>G		3_prime_UTR	Exon 7 of 7	NP_715639.2
	IL19	NM_001369605.1		c.*258A>G		3_prime_UTR	Exon 6 of 6	NP_001356534.1
	IL19	NM_001393490.1		c.*258A>G		3_prime_UTR	Exon 7 of 7	NP_001380419.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.*258A>G		3_prime_UTR	Exon 7 of 7	ENSP00000499459.2
	IL19	ENST00000340758.7	TSL:1	c.*258A>G		3_prime_UTR	Exon 6 of 6	ENSP00000343000.3
	IL19	ENST00000656872.2		c.*258A>G		3_prime_UTR	Exon 7 of 7	ENSP00000499487.2

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103969 AN: 152056 Hom.: 36548 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.690

GnomAD4 exome AF: 0.696 AC: 160883 AN: 231044 Hom.: 58342 Cov.: 0 AF XY: 0.693 AC XY: 82537 AN XY: 119114

African (AFR) AF: 0.587 AC: 4467 AN: 7612

American (AMR) AF: 0.620 AC: 5651 AN: 9108

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 6044 AN: 7636

East Asian (EAS) AF: 0.272 AC: 4575 AN: 16808

South Asian (SAS) AF: 0.635 AC: 13018 AN: 20488

European-Finnish (FIN) AF: 0.709 AC: 9360 AN: 13196

Middle Eastern (MID) AF: 0.706 AC: 771 AN: 1092

European-Non Finnish (NFE) AF: 0.759 AC: 107026 AN: 141018

Other (OTH) AF: 0.708 AC: 9971 AN: 14086

GnomAD4 genome AF: 0.684 AC: 104043 AN: 152174 Hom.: 36574 Cov.: 33 AF XY: 0.679 AC XY: 50531 AN XY: 74398

African (AFR) AF: 0.581 AC: 24116 AN: 41498

American (AMR) AF: 0.662 AC: 10119 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1682 AN: 5182

South Asian (SAS) AF: 0.653 AC: 3149 AN: 4820

European-Finnish (FIN) AF: 0.720 AC: 7626 AN: 10586

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52254 AN: 68002

Other (OTH) AF: 0.691 AC: 1459 AN: 2112

Alfa AF: 0.737 Hom.: 70056

Bravo AF: 0.668

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		0.19
Mutation Taster		=100/0	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

Other links and lift over

dbSNP: rs2243193; hg19: chr1-207016225; COSMIC: COSV54282970; COSMIC: COSV54282970;