1-206838140-G-A

Variant names:

• chr1-206838140-G-A
• rs2243174
• NM_153758.5:c.210+1117G>A

Variant summary

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

The NM_153758.5(IL19):​c.210+1117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,116 control chromosomes in the GnomAD database, including 37,163 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 0.69 (37163 hom., cov: 33)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	NM_153758.5	MANE Select	c.210+1117G>A		intron	N/A	NP_715639.2	Q9UHD0-1
	IL19	NM_001369605.1		c.210+1117G>A		intron	N/A	NP_001356534.1	Q9UHD0-1
	IL19	NM_001393490.1		c.210+1117G>A		intron	N/A	NP_001380419.1	Q9UHD0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.210+1117G>A		intron	N/A	ENSP00000499459.2	Q9UHD0-1
	IL19	ENST00000270218.10	TSL:1	c.210+1117G>A		intron	N/A	ENSP00000270218.6	Q9UHD0-1
	IL19	ENST00000340758.7	TSL:1	c.210+1117G>A		intron	N/A	ENSP00000343000.3	Q9UHD0-1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105066 AN: 151998 Hom.: 37122 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.691 AC: 105160 AN: 152116 Hom.: 37163 Cov.: 33 AF XY: 0.686 AC XY: 51004 AN XY: 74382

African (AFR) AF: 0.597 AC: 24741 AN: 41464

American (AMR) AF: 0.663 AC: 10142 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2729 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2058 AN: 5172

South Asian (SAS) AF: 0.659 AC: 3174 AN: 4820

European-Finnish (FIN) AF: 0.722 AC: 7643 AN: 10590

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52328 AN: 67996

Other (OTH) AF: 0.703 AC: 1484 AN: 2112

Alfa AF: 0.658 Hom.: 3455

Bravo AF: 0.676

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.014
DANN	Benign	0.72
PhyloP100		-3.0
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2243174;

hg19: chr1-207011485;

COSMIC: COSV54282937;