Variant chr6-137004764-TA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_014432.4(IL20RA):c.725-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.48 ( 16872 hom., cov: 0)

Exomes 𝑓: 0.42 ( 4758 hom. )

Failed GnomAD Quality Control

Consequence

IL20RA
NM_014432.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.60

Variant links:

Genes affected

IL20RA (HGNC:6003): (interleukin 20 receptor subunit alpha) This gene encodes a member of the type II cytokine receptor family. The encoded protein is a subunit of the receptor for interleukin 20, a cytokine that may be involved in epidermal function. The interleukin 20 receptor is a heterodimeric complex consisting of the encoded protein and interleukin 20 receptor beta. This gene and interleukin 20 receptor beta are highly expressed in skin, and are upregulated in psoriasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

IL20RA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 6-137004764-TA-T is Benign according to our data. Variant chr6-137004764-TA-T is described in ClinVar as [Benign]. Clinvar id is 402974.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL20RA	NM_014432.4 linkuse as main transcript	c.725-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10 linkuse as main transcript	c.725-5del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_014432.4	ENSP00000314976	P1	Q9UHF4-1
IL20RA	ENST00000367748.4 linkuse as main transcript	c.392-5del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000356722		Q9UHF4-2
IL20RA	ENST00000468393.5 linkuse as main transcript	c.392-5del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	4		ENSP00000489177
IL20RA	ENST00000541547.5 linkuse as main transcript	c.578-5del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000437843		Q9UHF4-3

Frequencies

GnomAD3 genomes

AF:

0.479

AC:

69737

AN:

145710

Hom.:

16870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.567

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.462

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.552

Gnomad OTH

AF:

0.489

GnomAD3 exomes

AF:

0.406

AC:

61501

AN:

151602

Hom.:

1665

AF XY:

0.409

AC XY:

34194

AN XY:

83602

show subpopulations

Gnomad AFR exome

AF:

0.361

Gnomad AMR exome

AF:

0.363

Gnomad ASJ exome

AF:

0.388

Gnomad EAS exome

AF:

0.299

Gnomad SAS exome

AF:

0.416

Gnomad FIN exome

AF:

0.389

Gnomad NFE exome

AF:

0.436

Gnomad OTH exome

AF:

0.410

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.421

AC:

522335

AN:

1239266

Hom.:

4758

Cov.:

AF XY:

0.421

AC XY:

259762

AN XY:

617592

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.338

Gnomad4 ASJ exome

AF:

0.390

Gnomad4 EAS exome

AF:

0.264

Gnomad4 SAS exome

AF:

0.408

Gnomad4 FIN exome

AF:

0.378

Gnomad4 NFE exome

AF:

0.436

Gnomad4 OTH exome

AF:

0.410

GnomAD4 genome

AF:

0.479

AC:

69759

AN:

145756

Hom.:

16872

Cov.:

AF XY:

0.470

AC XY:

33233

AN XY:

70726

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.454

Gnomad4 ASJ

AF:

0.462

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.552

Gnomad4 OTH

AF:

0.486

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over