rs2981572

Variant names:

• chr1-206864800-G-T
• rs2981572
• NM_001385166.1:c.-170-747G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385166.1(IL20):​c.-170-747G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,924 control chromosomes in the GnomAD database, including 21,927 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 0.52 (21927 hom., cov: 32)
• Consequence: IL20 NM_001385166.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 14 publications found

Genes affected

IL20 (HGNC:6002): (interleukin 20) The protein encoded by this gene is a cytokine structurally related to interleukin 10 (IL10). This cytokine has been shown to transduce its signal through signal transducer and activator of transcription 3 (STAT3) in keratinocytes. A specific receptor for this cytokine is found to be expressed in skin and upregulated dramatically in psoriatic skin, suggesting a role for this protein in epidermal function and psoriasis. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20	NM_001385166.1	c.-170-747G>T		intron_variant	Intron 1 of 6		NP_001372095.1
IL20	NM_001385167.1	c.-251-546G>T		intron_variant	Intron 1 of 7		NP_001372096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79582 AN: 151806 Hom.: 21918 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.524 AC: 79618 AN: 151924 Hom.: 21927 Cov.: 32 AF XY: 0.516 AC XY: 38338 AN XY: 74252

African (AFR) AF: 0.448 AC: 18540 AN: 41420

American (AMR) AF: 0.434 AC: 6620 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3466

East Asian (EAS) AF: 0.155 AC: 803 AN: 5168

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4812

European-Finnish (FIN) AF: 0.610 AC: 6421 AN: 10526

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42184 AN: 67968

Other (OTH) AF: 0.509 AC: 1074 AN: 2108

Alfa AF: 0.572 Hom.: 3426

Bravo AF: 0.503

Asia WGS AF: 0.250 AC: 870 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs2981572; hg19: chr1-207038145; COSMIC: COSV65584359;