rs2228046

Variant names:

Variant summary

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

The NM_002184.4(IL6ST):c.1361T>C(p.Ile454Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0158 in 1,612,922 control chromosomes in the GnomAD database, including 3,480 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 1852 hom., cov: 32)

Exomes 𝑓: 0.0086 ( 1628 hom. )

Consequence

IL6ST
NM_002184.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 6.33

Publications

19 publications found

Variant links:

COSMIC-nc: COSV61140364

Genes affected

IL6ST (HGNC:6021): (interleukin 6 cytokine family signal transducer) The protein encoded by this gene is a signal transducer shared by many cytokines, including interleukin 6 (IL6), ciliary neurotrophic factor (CNTF), leukemia inhibitory factor (LIF), and oncostatin M (OSM). This protein functions as a part of the cytokine receptor complex. The activation of this protein is dependent upon the binding of cytokines to their receptors. vIL6, a protein related to IL6 and encoded by the Kaposi sarcoma-associated herpesvirus, can bypass the interleukin 6 receptor (IL6R) and directly activate this protein. Knockout studies in mice suggest that this gene plays a critical role in regulating myocyte apoptosis. Alternatively spliced transcript variants have been described. A related pseudogene has been identified on chromosome 17. [provided by RefSeq, May 2014]

IL6ST Gene-Disease associations (from GenCC):

hyper-IgE recurrent infection syndrome 4A, autosomal dominant
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
hyper-IgE recurrent infection syndrome 4, autosomal recessive
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

IL6ST 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 (MetaRNN=0.004338354).

BP6

Variant 5-55954899-A-G is Benign according to our data. Variant chr5-55954899-A-G is described in ClinVar as Benign. ClinVar VariationId is 1170115.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002184.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
IL6ST	NM_002184.4	MANE Select	c.1361T>C	p.Ile454Thr	missense	Exon 11 of 17	NP_002175.2
IL6ST	NM_001364275.2		c.1361T>C	p.Ile454Thr	missense	Exon 11 of 16	NP_001351204.1	A0A0A0N0L5
IL6ST	NM_001364276.2		c.1151T>C	p.Ile384Thr	missense	Exon 11 of 17	NP_001351205.1	A0A8V8TMJ9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
IL6ST	ENST00000381298.7	TSL:1 MANE Select	c.1361T>C	p.Ile454Thr	missense	Exon 11 of 17	ENSP00000370698.2	P40189-1
IL6ST	ENST00000522633.2	TSL:1	c.*288T>C		3_prime_UTR	Exon 9 of 13	ENSP00000435399.1	P40189-2
IL6ST	ENST00000381294.8	TSL:1	c.1267+1126T>C		intron	N/A	ENSP00000370694.3	P40189-3

Frequencies

GnomAD3 genomes

AF:

0.0846

AC:

12874

AN:

152142

Hom.:

1846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0342

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000413

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000926

Gnomad OTH

AF:

0.0645

GnomAD2 exomes

AF:

0.0214

AC:

5373

AN:

251074

AF XY:

0.0153

show subpopulations

Gnomad AFR exome

AF:

0.294

Gnomad AMR exome

AF:

0.0131

Gnomad ASJ exome

AF:

0.000198

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000590

Gnomad OTH exome

AF:

0.0123

GnomAD4 exome

AF:

0.00860

AC:

12560

AN:

1460662

Hom.:

1628

Cov.:

AF XY:

0.00735

AC XY:

5342

AN XY:

726722

show subpopulations

African (AFR)

AF:

0.300

AC:

10003

AN:

33388

American (AMR)

AF:

0.0151

AC:

676

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.0000765

AC:

AN:

26128

East Asian (EAS)

AF:

0.00

AC:

AN:

39676

South Asian (SAS)

AF:

0.000766

AC:

AN:

86166

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53416

Middle Eastern (MID)

AF:

0.0139

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.000445

AC:

494

AN:

1111080

Other (OTH)

AF:

0.0205

AC:

1239

AN:

60344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

446

892

1338

1784

2230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.0848

AC:

12919

AN:

152260

Hom.:

1852

Cov.:

AF XY:

0.0821

AC XY:

6115

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.294

AC:

12195

AN:

41494

American (AMR)

AF:

0.0341

AC:

522

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.000414

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000926

AC:

AN:

68030

Other (OTH)

AF:

0.0639

AC:

135

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

464

927

1391

1854

2318

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0170

Hom.:

620

Bravo

AF:

0.0964

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.282

AC:

1244

ESP6500EA

AF:

0.000581

AC:

ExAC

AF:

0.0265

AC:

3215

Asia WGS

AF:

0.0160

AC:

AN:

3476

EpiCase

AF:

0.00120

EpiControl

AF:

0.000652

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

IL6ST-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.61

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.58

Eigen

Benign

-0.020

Eigen_PC

Benign

0.018

FATHMM_MKL

Benign

0.62

LIST_S2

Uncertain

0.89

MetaRNN

Benign

0.0043

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

PhyloP100

6.3

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-2.9

REVEL

Benign

0.15

Sift

Uncertain

0.0040

Sift4G

Uncertain

0.0060

Polyphen

0.31

Vest4

0.53

MPC

0.40

ClinPred

0.046

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.42

gMVP

0.81

Mutation Taster

=90/10

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