1-206865341-C-T

Variant names:

• chr1-206865341-C-T
• rs1400986
• NM_001385166.1:c.-170-206C>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.-170-206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 211,238 control chromosomes in the GnomAD database, including 5,928 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 0.23 (4987 hom., cov: 32)
  • Exomes 𝑓: 0.17 (941 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20	NM_001385166.1	c.-170-206C>T		intron_variant	Intron 1 of 6		NP_001372095.1
IL20	NM_001385167.1	c.-251-5C>T		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 AF: 0.233 AC: 35357 AN: 152006 Hom.: 4963 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.170 AC: 10068 AN: 59114 Hom.: 941 Cov.: 4 AF XY: 0.173 AC XY: 4947 AN XY: 28650

African (AFR) AF: 0.403 AC: 434 AN: 1076

American (AMR) AF: 0.196 AC: 54 AN: 276

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 109 AN: 416

East Asian (EAS) AF: 0.172 AC: 70 AN: 408

South Asian (SAS) AF: 0.352 AC: 419 AN: 1192

European-Finnish (FIN) AF: 0.0773 AC: 17 AN: 220

Middle Eastern (MID) AF: 0.254 AC: 32 AN: 126

European-Non Finnish (NFE) AF: 0.160 AC: 8572 AN: 53464

Other (OTH) AF: 0.186 AC: 361 AN: 1936

GnomAD4 genome AF: 0.233 AC: 35426 AN: 152124 Hom.: 4987 Cov.: 32 AF XY: 0.233 AC XY: 17341 AN XY: 74378

African (AFR) AF: 0.370 AC: 15349 AN: 41478

American (AMR) AF: 0.248 AC: 3782 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3472

East Asian (EAS) AF: 0.171 AC: 885 AN: 5174

South Asian (SAS) AF: 0.355 AC: 1713 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10594

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10597 AN: 67982

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.190 Hom.: 4939

Bravo AF: 0.248

Asia WGS AF: 0.318 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.35
PromoterAI		0.0075	Neutral
Mutation Taster		=100/0	polymorphism

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;