rs2981572

chr1-206864800-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

IL20 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IL20	NM_001385166.1	c.-170-747G>T		intron_variant
IL20	NM_001385167.1	c.-251-546G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.509

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

Splicing

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

Publications

LitVar

Other links and lift over

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