NM_153758.5:c.-149+13026T>C

Variant names:

• chr1-206784104-T-C
• rs4072226
• NM_153758.5:c.-149+13026T>C

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+13026T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,028 control chromosomes in the GnomAD database, including 29,414 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 (29414 hom., cov: 31)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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.-149+13026T>C		intron	N/A	NP_715639.2
	IL19	NM_001393490.1		c.-149+13274T>C		intron	N/A	NP_001380419.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.-149+13026T>C		intron	N/A	ENSP00000499459.2
	IL19	ENST00000656872.2		c.-149+13274T>C		intron	N/A	ENSP00000499487.2
	IL19	ENST00000662320.1		n.67+13274T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93231 AN: 151910 Hom.: 29398 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.614 AC: 93270 AN: 152028 Hom.: 29414 Cov.: 31 AF XY: 0.621 AC XY: 46148 AN XY: 74308

African (AFR) AF: 0.542 AC: 22454 AN: 41432

American (AMR) AF: 0.745 AC: 11388 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2491 AN: 3464

East Asian (EAS) AF: 0.975 AC: 5052 AN: 5182

South Asian (SAS) AF: 0.778 AC: 3748 AN: 4816

European-Finnish (FIN) AF: 0.577 AC: 6099 AN: 10576

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39905 AN: 67962

Other (OTH) AF: 0.653 AC: 1375 AN: 2106

Alfa AF: 0.608 Hom.: 20100

Bravo AF: 0.622

Asia WGS AF: 0.808 AC: 2812 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	0.76
DANN	Benign	0.76
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4072226; hg19: chr1-206957449; COSMIC: COSV60019535;