1-206789071-C-T

Variant names:

• chr1-206789071-C-T
• rs885334
• NM_153758.5:c.-148-9790C>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.-148-9790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,024 control chromosomes in the GnomAD database, including 29,486 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 0.61 (29486 hom., cov: 31)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.-148-9790C>T		intron_variant	Intron 1 of 6	ENST00000659997.3	NP_715639.2
IL19	NM_001393490.1	c.-148-9790C>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.-148-9790C>T		intron_variant	Intron 1 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000656872.2	c.-148-9790C>T		intron_variant	Intron 1 of 6			ENSP00000499487.2
IL19	ENST00000662320.1	n.68-9790C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92796 AN: 151906 Hom.: 29488 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.611 AC: 92815 AN: 152024 Hom.: 29486 Cov.: 31 AF XY: 0.607 AC XY: 45130 AN XY: 74314

African (AFR) AF: 0.436 AC: 18077 AN: 41432

American (AMR) AF: 0.612 AC: 9352 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2471 AN: 3468

East Asian (EAS) AF: 0.701 AC: 3626 AN: 5172

South Asian (SAS) AF: 0.532 AC: 2561 AN: 4816

European-Finnish (FIN) AF: 0.651 AC: 6875 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47797 AN: 67974

Other (OTH) AF: 0.614 AC: 1295 AN: 2108

Alfa AF: 0.669 Hom.: 151744

Bravo AF: 0.600

Asia WGS AF: 0.527 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
DANN	Benign	0.58
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs885334; hg19: chr1-206962416;