1-206829974-G-T

Variant names:

• chr1-206829974-G-T
• rs4845143
• NM_153758.5:c.-2-6687G>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.-2-6687G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,126 control chromosomes in the GnomAD database, including 40,392 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 0.72 (40392 hom., cov: 32)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 16 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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.-2-6687G>T		intron_variant	Intron 2 of 6	ENST00000659997.3	NP_715639.2
IL19	NM_001393490.1	c.-2-6687G>T		intron_variant	Intron 2 of 6		NP_001380419.1
IL19	NM_001393491.1	c.-3+848G>T		intron_variant	Intron 1 of 5		NP_001380420.1
IL19	NM_013371.5	c.-690+848G>T		intron_variant	Intron 1 of 6		NP_037503.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000659997.3	c.-2-6687G>T		intron_variant	Intron 2 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000270218.10	c.-690+848G>T		intron_variant	Intron 1 of 6	1		ENSP00000270218.6
IL19	ENST00000656872.2	c.-2-6687G>T		intron_variant	Intron 2 of 6			ENSP00000499487.2

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109940 AN: 152008 Hom.: 40343 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.723 AC: 110042 AN: 152126 Hom.: 40392 Cov.: 32 AF XY: 0.716 AC XY: 53257 AN XY: 74382

African (AFR) AF: 0.665 AC: 27584 AN: 41476

American (AMR) AF: 0.671 AC: 10252 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2716 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2255 AN: 5184

South Asian (SAS) AF: 0.672 AC: 3238 AN: 4820

European-Finnish (FIN) AF: 0.727 AC: 7696 AN: 10580

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.793 AC: 53887 AN: 67994

Other (OTH) AF: 0.723 AC: 1529 AN: 2114

Alfa AF: 0.762 Hom.: 24879

Bravo AF: 0.710

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.81
PhyloP100		-0.089
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: rs4845143; hg19: chr1-207003319; COSMIC: COSV54282920; COSMIC: COSV54282920;