ENST00000270218.10:c.-107C>G

Variant names:

• chr1-206834296-C-G
• rs2243158
• ENST00000270218.10:c.-107C>G

Variant summary

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

The ENST00000270218.10(IL19):​c.-107C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 985,412 control chromosomes in the GnomAD database, including 404,556 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 0.89 (59925 hom., cov: 32)
  • Exomes 𝑓: 0.91 (344631 hom.)
• Consequence: IL19 ENST00000270218.10 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 17 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=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000270218.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	NM_153758.5	MANE Select	c.-2-2365C>G		intron	N/A	NP_715639.2	Q9UHD0-1
	IL19	NM_013371.5		c.-107C>G		5_prime_UTR	Exon 2 of 7	NP_037503.2
	IL19	NM_001393490.1		c.-2-2365C>G		intron	N/A	NP_001380419.1	Q9UHD0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000270218.10	TSL:1	c.-107C>G		5_prime_UTR	Exon 2 of 7	ENSP00000270218.6	Q9UHD0-1
	IL19	ENST00000659997.3	MANE Select	c.-2-2365C>G		intron	N/A	ENSP00000499459.2	Q9UHD0-1
	IL19	ENST00000656872.2		c.-2-2365C>G		intron	N/A	ENSP00000499487.2	Q9UHD0-1

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134844 AN: 152138 Hom.: 59867 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.890

GnomAD4 exome AF: 0.909 AC: 757719 AN: 833156 Hom.: 344631 Cov.: 36 AF XY: 0.910 AC XY: 350079 AN XY: 384752

African (AFR) AF: 0.856 AC: 13504 AN: 15778

American (AMR) AF: 0.881 AC: 867 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 4703 AN: 5148

East Asian (EAS) AF: 0.803 AC: 3024 AN: 3768

South Asian (SAS) AF: 0.920 AC: 15145 AN: 16456

European-Finnish (FIN) AF: 0.878 AC: 253 AN: 288

Middle Eastern (MID) AF: 0.881 AC: 1428 AN: 1620

European-Non Finnish (NFE) AF: 0.911 AC: 694155 AN: 761820

Other (OTH) AF: 0.903 AC: 24640 AN: 27294

GnomAD4 genome AF: 0.886 AC: 134960 AN: 152256 Hom.: 59925 Cov.: 32 AF XY: 0.885 AC XY: 65856 AN XY: 74420

African (AFR) AF: 0.855 AC: 35507 AN: 41538

American (AMR) AF: 0.871 AC: 13328 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3184 AN: 3472

East Asian (EAS) AF: 0.784 AC: 4058 AN: 5176

South Asian (SAS) AF: 0.911 AC: 4394 AN: 4822

European-Finnish (FIN) AF: 0.901 AC: 9543 AN: 10596

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.911 AC: 61963 AN: 68040

Other (OTH) AF: 0.890 AC: 1882 AN: 2114

Alfa AF: 0.900 Hom.: 29573

Bravo AF: 0.879

Asia WGS AF: 0.833 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		-0.38
PromoterAI		0.011	Neutral
Mutation Taster		=300/0	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: rs2243158; hg19: chr1-207007641;