NM_153758.5:c.-3+16716T>C

Variant names:

• chr1-206815722-T-C
• rs12046559
• NM_153758.5:c.-3+16716T>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.-3+16716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,900 control chromosomes in the GnomAD database, including 2,436 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 0.16 (2436 hom., cov: 32)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.-3+16716T>C		intron_variant	Intron 2 of 6	ENST00000659997.3	NP_715639.2
IL19	NM_001393490.1	c.-3+16716T>C		intron_variant	Intron 2 of 6		NP_001380419.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000659997.3	c.-3+16716T>C		intron_variant	Intron 2 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000656872.2	c.-3+16716T>C		intron_variant	Intron 2 of 6			ENSP00000499487.2
IL19	ENST00000662320.1	n.214-9768T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24407 AN: 151782 Hom.: 2427 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.161 AC: 24434 AN: 151900 Hom.: 2436 Cov.: 32 AF XY: 0.167 AC XY: 12377 AN XY: 74258

African (AFR) AF: 0.197 AC: 8144 AN: 41394

American (AMR) AF: 0.228 AC: 3485 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3466

East Asian (EAS) AF: 0.475 AC: 2454 AN: 5162

South Asian (SAS) AF: 0.202 AC: 971 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1309 AN: 10542

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7125 AN: 67946

Other (OTH) AF: 0.165 AC: 347 AN: 2102

Alfa AF: 0.124 Hom.: 3020

Bravo AF: 0.172

Asia WGS AF: 0.314 AC: 1093 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.33
PhyloP100		-0.0070
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: rs12046559; hg19: chr1-206989067;