rs1400986

Variant names:

• chr1-206865341-C-A
• rs1400986
• NM_001385166.1:c.-170-206C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-206865341-C-A
• chr1-206865341-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001385166.1(IL20):​c.-170-206C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 59,248 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.000017 (0 hom.)
• Consequence: IL20 NM_001385166.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 19 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20	NM_001385166.1	c.-170-206C>A		intron_variant	Intron 1 of 6		NP_001372095.1
IL20	NM_001385167.1	c.-251-5C>A		splice_region_variant, 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 Cov.: 32

GnomAD4 exome AF: 0.0000169 AC: 1 AN: 59248 Hom.: 0 Cov.: 4 AF XY: 0.0000348 AC XY: 1 AN XY: 28714

African (AFR) AF: 0.00 AC: 0 AN: 1084

American (AMR) AF: 0.00 AC: 0 AN: 276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 418

East Asian (EAS) AF: 0.00 AC: 0 AN: 410

South Asian (SAS) AF: 0.00 AC: 0 AN: 1196

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 222

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 126

European-Non Finnish (NFE) AF: 0.0000187 AC: 1 AN: 53578

Other (OTH) AF: 0.00 AC: 0 AN: 1938

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		-0.35
PromoterAI		-0.0025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1400986; hg19: chr1-207038686;