dbSNP rs7281762: IL10RB:c.804+9006G>A (chr21-33297267-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001405850.1(IL10RB):c.804+9006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,972 control chromosomes in the GnomAD database, including 2,365 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 0.16 ( 2365 hom., cov: 30)

Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

IL10RB
NM_001405850.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Variant links:

Genes affected

IL10RB (HGNC:5965): (interleukin 10 receptor subunit beta) The protein encoded by this gene belongs to the cytokine receptor family. It is an accessory chain essential for the active interleukin 10 receptor complex. Coexpression of this and IL10RA proteins has been shown to be required for IL10-induced signal transduction. This gene and three other interferon receptor genes, IFAR2, IFNAR1, and IFNGR2, form a class II cytokine receptor gene cluster located in a small region on chromosome 21. [provided by RefSeq, Jul 2008]

IL10RB links:

IFNAR2-IL10RB (HGNC:):

IFNAR2-IL10RB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL10RB	NM_000628.5 link	c.*910G>A		downstream_gene_variant		ENST00000290200.7	NP_000619.3	Q08334

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL10RB	ENST00000290200.7 link	c.*910G>A		downstream_gene_variant		1	NM_000628.5	ENSP00000290200.2		Q08334

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23635

AN:

151778

Hom.:

2371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0389

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.361

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.154

GnomAD4 exome

AF:

0.145

AC:

AN:

Hom.:

Cov.:

AF XY:

0.111

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.155

AC:

23619

AN:

151896

Hom.:

2365

Cov.:

AF XY:

0.160

AC XY:

11904

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.0388

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.360

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.190

Gnomad4 OTH

AF:

0.152

Alfa

AF:

0.134

Hom.:

397

Bravo

AF:

0.145

Asia WGS

AF:

0.323

AC:

1121

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

7.8

DANN

Benign

0.55

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over