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GeneBe

3-136989562-C-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_144717.4(IL20RB):c.528C>G(p.Ala176=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00212 in 1,613,696 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 5 hom. )

Consequence

IL20RB
NM_144717.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0510
Variant links:
Genes affected
IL20RB (HGNC:6004): (interleukin 20 receptor subunit beta) IL20RB and IL20RA (MIM 605620) form a heterodimeric receptor for interleukin-20 (IL20; MIM 605619) (Blumberg et al., 2001 [PubMed 11163236]).[supplied by OMIM, Feb 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-136989562-C-G is Benign according to our data. Variant chr3-136989562-C-G is described in ClinVar as [Benign]. Clinvar id is 774849.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.051 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL20RBNM_144717.4 linkuse as main transcriptc.528C>G p.Ala176= synonymous_variant 4/7 ENST00000329582.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL20RBENST00000329582.9 linkuse as main transcriptc.528C>G p.Ala176= synonymous_variant 4/71 NM_144717.4 P1Q6UXL0-1
IL20RBENST00000475972.1 linkuse as main transcriptc.*160C>G 3_prime_UTR_variant, NMD_transcript_variant 4/71
IL20RBENST00000469964.5 linkuse as main transcriptc.*513C>G 3_prime_UTR_variant, NMD_transcript_variant 4/62
IL20RBENST00000491483.5 linkuse as main transcriptc.*513C>G 3_prime_UTR_variant, NMD_transcript_variant 4/65

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00159
AC:
242
AN:
152130
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000459
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00157
Gnomad ASJ
AF:
0.00230
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00260
Gnomad OTH
AF:
0.00430
GnomAD3 exomes
AF:
0.00165
AC:
413
AN:
251002
Hom.:
3
AF XY:
0.00192
AC XY:
261
AN XY:
135684
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.00127
Gnomad ASJ exome
AF:
0.00189
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00137
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.00259
Gnomad OTH exome
AF:
0.00163
GnomAD4 exome
AF:
0.00217
AC:
3171
AN:
1461448
Hom.:
5
Cov.:
31
AF XY:
0.00218
AC XY:
1587
AN XY:
727024
show subpopulations
Gnomad4 AFR exome
AF:
0.000299
Gnomad4 AMR exome
AF:
0.00141
Gnomad4 ASJ exome
AF:
0.00199
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00107
Gnomad4 FIN exome
AF:
0.000225
Gnomad4 NFE exome
AF:
0.00244
Gnomad4 OTH exome
AF:
0.00346
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00159
AC:
242
AN:
152248
Hom.:
0
Cov.:
32
AF XY:
0.00149
AC XY:
111
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.000457
Gnomad4 AMR
AF:
0.00157
Gnomad4 ASJ
AF:
0.00230
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00260
Gnomad4 OTH
AF:
0.00426
Alfa
AF:
0.00141
Hom.:
1
Bravo
AF:
0.00169
EpiCase
AF:
0.00414
EpiControl
AF:
0.00356

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 11, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
0.95
Dann
Benign
0.44

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs244405; hg19: chr3-136708404; API