1-206776020-A-T

Variant names:

• chr1-206776020-A-T
• rs1800890
• NM_153758.5:c.-149+4942A>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+4942A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,032 control chromosomes in the GnomAD database, including 8,198 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 0.31 (8198 hom., cov: 32)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 197 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	NM_153758.5	MANE Select	c.-149+4942A>T		intron	N/A	NP_715639.2
	IL19	NM_001393490.1		c.-149+5190A>T		intron	N/A	NP_001380419.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.-149+4942A>T		intron	N/A	ENSP00000499459.2
	IL19	ENST00000656872.2		c.-149+5190A>T		intron	N/A	ENSP00000499487.2
	IL19	ENST00000662320.1		n.67+5190A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47598 AN: 151914 Hom.: 8196 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.313 AC: 47614 AN: 152032 Hom.: 8198 Cov.: 32 AF XY: 0.306 AC XY: 22724 AN XY: 74310

African (AFR) AF: 0.243 AC: 10079 AN: 41446

American (AMR) AF: 0.228 AC: 3494 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3472

East Asian (EAS) AF: 0.0258 AC: 134 AN: 5186

South Asian (SAS) AF: 0.203 AC: 976 AN: 4812

European-Finnish (FIN) AF: 0.372 AC: 3933 AN: 10560

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26849 AN: 67950

Other (OTH) AF: 0.290 AC: 611 AN: 2108

Alfa AF: 0.229 Hom.: 537

Bravo AF: 0.300

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1800890; hg19: chr1-206949365;