1-206786871-C-T

Position:

• chr1-206786871-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153758.5(IL19):​c.-148-11990C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,962 control chromosomes in the GnomAD database, including 36,473 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 0.68 (36473 hom., cov: 30)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL19	NM_153758.5	c.-148-11990C>T		intron_variant		ENST00000659997.3
IL19	NM_001393490.1	c.-148-11990C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL19	ENST00000659997.3	c.-148-11990C>T		intron_variant			NM_153758.5	P1
IL19	ENST00000656872.2	c.-148-11990C>T		intron_variant				P1
IL19	ENST00000662320.1	n.68-11990C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103484 AN: 151844 Hom.: 36465 Cov.: 30

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.681 AC: 103516 AN: 151962 Hom.: 36473 Cov.: 30 AF XY: 0.678 AC XY: 50324 AN XY: 74276

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.690

Alfa AF: 0.757 Hom.: 34236

Bravo AF: 0.669

Asia WGS AF: 0.576 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs880790; hg19: chr1-206960216;