NM_153758.5:c.-149+11693G>T

Variant names:

• chr1-206782771-G-T
• rs61815643
• NM_153758.5:c.-149+11693G>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.-149+11693G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,136 control chromosomes in the GnomAD database, including 1,075 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 0.11 (1075 hom., cov: 32)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.-149+11693G>T		intron_variant	Intron 1 of 6	ENST00000659997.3	NP_715639.2
IL19	NM_001393490.1	c.-149+11941G>T		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.-149+11693G>T		intron_variant	Intron 1 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000656872.2	c.-149+11941G>T		intron_variant	Intron 1 of 6			ENSP00000499487.2
IL19	ENST00000662320.1	n.67+11941G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16546 AN: 152018 Hom.: 1075 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.109 AC: 16543 AN: 152136 Hom.: 1075 Cov.: 32 AF XY: 0.107 AC XY: 7970 AN XY: 74358

African (AFR) AF: 0.0557 AC: 2311 AN: 41522

American (AMR) AF: 0.0721 AC: 1102 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5186

South Asian (SAS) AF: 0.0939 AC: 452 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1854 AN: 10568

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10030 AN: 67980

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.0431 Hom.: 41

Bravo AF: 0.0988

Asia WGS AF: 0.0620 AC: 214 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	0.21
DANN	Benign	0.60
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs61815643; hg19: chr1-206956116;