dbSNP rs1058867: IL10RB:c.*719G>A (chr21-33297076-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000628.5(IL10RB):c.*719G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 160,450 control chromosomes in the GnomAD database, including 24,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 23022 hom., cov: 30)

Exomes 𝑓: 0.59 ( 1613 hom. )

Consequence

IL10RB
NM_000628.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.660

Publications

37 publications found

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 Gene-Disease associations (from GenCC):

inflammatory bowel disease 25
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
IL10-related early-onset inflammatory bowel disease
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

IL10RB links:

IFNAR2-IL10RB (HGNC:):

IFNAR2-IL10RB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 21-33297076-G-A is Benign according to our data. Variant chr21-33297076-G-A is described in ClinVar as Benign. ClinVar VariationId is 339709.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000628.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL10RB	NM_000628.5	MANE Select	c.*719G>A	3_prime_UTR	Exon 7 of 7	NP_000619.3
IFNAR2-IL10RB	NM_001414505.1		c.*719G>A	3_prime_UTR	Exon 13 of 13	NP_001401434.1	H0Y3Z8
IL10RB	NM_001406840.1		c.*870G>A	3_prime_UTR	Exon 6 of 6	NP_001393769.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL10RB	ENST00000290200.7	TSL:1 MANE Select	c.*719G>A	3_prime_UTR	Exon 7 of 7	ENSP00000290200.2	Q08334
IL10RB	ENST00000896213.1		c.*719G>A	3_prime_UTR	Exon 7 of 7	ENSP00000566272.1
IL10RB	ENST00000896212.1		c.*719G>A	3_prime_UTR	Exon 7 of 7	ENSP00000566271.1

Frequencies

GnomAD3 genomes

AF:

0.537

AC:

81495

AN:

151690

Hom.:

23031

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.747

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.556

GnomAD4 exome

AF:

0.592

AC:

5116

AN:

8642

Hom.:

1613

Cov.:

AF XY:

0.588

AC XY:

2603

AN XY:

4426

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.598

AC:

973

AN:

1628

Ashkenazi Jewish (ASJ)

AF:

0.452

AC:

AN:

East Asian (EAS)

AF:

0.670

AC:

264

AN:

394

South Asian (SAS)

AF:

0.655

AC:

642

AN:

980

European-Finnish (FIN)

AF:

0.559

AC:

AN:

118

Middle Eastern (MID)

AF:

0.400

AC:

AN:

European-Non Finnish (NFE)

AF:

0.579

AC:

2929

AN:

5058

Other (OTH)

AF:

0.580

AC:

203

AN:

350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

103

206

308

411

514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

124

186

248

310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.537

AC:

81494

AN:

151808

Hom.:

23022

Cov.:

AF XY:

0.542

AC XY:

40195

AN XY:

74174

show subpopulations

African (AFR)

AF:

0.357

AC:

14774

AN:

41340

American (AMR)

AF:

0.581

AC:

8870

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.475

AC:

1649

AN:

3470

East Asian (EAS)

AF:

0.746

AC:

3860

AN:

5172

South Asian (SAS)

AF:

0.663

AC:

3188

AN:

4812

European-Finnish (FIN)

AF:

0.655

AC:

6867

AN:

10486

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.594

AC:

40356

AN:

67932

Other (OTH)

AF:

0.557

AC:

1179

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1818

3637

5455

7274

9092

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.570

Hom.:

79513

Bravo

AF:

0.524

Asia WGS

AF:

0.705

AC:

2451

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Inflammatory bowel disease 25 (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.48

(source)

DANN

Benign

0.51

PhyloP100

-0.66

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over