Variant rs2243188 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153758.5(IL19):c.438+49A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 1,485,528 control chromosomes in the GnomAD database, including 407,337 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 ( 37090 hom., cov: 32)

Exomes 𝑓: 0.74 ( 370247 hom. )

Consequence

IL19
NM_153758.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Variant links:

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]

IL19 links:

LOC105372878 (HGNC:):

LOC105372878 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL19	NM_153758.5 linkuse as main transcript	c.438+49A>C		intron_variant		ENST00000659997.3	NP_715639.2
LOC105372878	XR_922482.3 linkuse as main transcript	n.701T>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000659997.3 linkuse as main transcript	c.438+49A>C	intron_variant		NM_153758.5	ENSP00000499459	P1	Q9UHD0-1
IL19	ENST00000270218.10 linkuse as main transcript	c.438+49A>C	intron_variant	1		ENSP00000270218	P1	Q9UHD0-1
IL19	ENST00000340758.7 linkuse as main transcript	c.438+49A>C	intron_variant	1		ENSP00000343000	P1	Q9UHD0-1
IL19	ENST00000656872.2 linkuse as main transcript	c.438+49A>C	intron_variant			ENSP00000499487	P1	Q9UHD0-1

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104911

AN:

152010

Hom.:

37049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.589

Gnomad AMI

AF:

0.721

Gnomad AMR

AF:

0.663

Gnomad ASJ

AF:

0.789

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.721

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.700

GnomAD3 exomes

AF:

0.690

AC:

171225

AN:

248016

Hom.:

60597

AF XY:

0.698

AC XY:

93554

AN XY:

134084

show subpopulations

Gnomad AFR exome

AF:

0.587

Gnomad AMR exome

AF:

0.605

Gnomad ASJ exome

AF:

0.789

Gnomad EAS exome

AF:

0.384

Gnomad SAS exome

AF:

0.697

Gnomad FIN exome

AF:

0.720

Gnomad NFE exome

AF:

0.763

Gnomad OTH exome

AF:

0.721

GnomAD4 exome

AF:

0.741

AC:

987459

AN:

1333400

Hom.:

370247

Cov.:

AF XY:

0.740

AC XY:

495739

AN XY:

670050

show subpopulations

Gnomad4 AFR exome

AF:

0.592

Gnomad4 AMR exome

AF:

0.610

Gnomad4 ASJ exome

AF:

0.789

Gnomad4 EAS exome

AF:

0.362

Gnomad4 SAS exome

AF:

0.693

Gnomad4 FIN exome

AF:

0.719

Gnomad4 NFE exome

AF:

0.771

Gnomad4 OTH exome

AF:

0.724

GnomAD4 genome

AF:

0.690

AC:

105005

AN:

152128

Hom.:

37090

Cov.:

AF XY:

0.685

AC XY:

50946

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.590

Gnomad4 AMR

AF:

0.663

Gnomad4 ASJ

AF:

0.789

Gnomad4 EAS

AF:

0.399

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.721

Gnomad4 NFE

AF:

0.770

Gnomad4 OTH

AF:

0.701

Alfa

AF:

0.698

Hom.:

6001

Bravo

AF:

0.674

Asia WGS

AF:

0.562

AC:

1954

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

DANN

Benign

0.58

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over