Variant 7-22727026-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_131935.1(IL6-AS1):n.54-321G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 554,376 control chromosomes in the GnomAD database, including 131,638 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other,risk factor (no stars).

Frequency

Genomes: 𝑓 0.72 ( 41246 hom., cov: 29)

Exomes 𝑓: 0.65 ( 90392 hom. )

Consequence

IL6-AS1
NR_131935.1 intron, non_coding_transcript

Scores

Clinical Significance

other; risk factor no assertion criteria provided O:7

Conservation

PhyloP100: 3.25

Variant links:

Genes affected

IL6-AS1 (HGNC:40301): (IL6 antisense RNA 1)

IL6-AS1 links:

IL6 (HGNC:6018): (interleukin 6) This gene encodes a cytokine that functions in inflammation and the maturation of B cells. In addition, the encoded protein has been shown to be an endogenous pyrogen capable of inducing fever in people with autoimmune diseases or infections. The protein is primarily produced at sites of acute and chronic inflammation, where it is secreted into the serum and induces a transcriptional inflammatory response through interleukin 6 receptor, alpha. The functioning of this gene is implicated in a wide variety of inflammation-associated disease states, including suspectibility to diabetes mellitus and systemic juvenile rheumatoid arthritis. Elevated levels of the encoded protein have been found in virus infections, including COVID-19 (disease caused by SARS-CoV-2). [provided by RefSeq, Aug 2020]

IL6 links:

STEAP1B (HGNC:41907): (STEAP family member 1B) Predicted to be integral component of membrane. Predicted to be active in endosome and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

STEAP1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL6-AS1	NR_131935.1 linkuse as main transcript	n.54-321G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Appris
IL6-AS1	ENST00000325042.2 linkuse as main transcript	n.54-321G>C	intron_variant, non_coding_transcript_variant	1
IL6	ENST00000404625.5 linkuse as main transcript	c.-84-153C>G	intron_variant	5	P1
STEAP1B	ENST00000650428.1 linkuse as main transcript	n.46+542G>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108695

AN:

151800

Hom.:

41177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.927

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.789

Gnomad ASJ

AF:

0.737

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.841

Gnomad FIN

AF:

0.476

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.738

GnomAD4 exome

AF:

0.652

AC:

262377

AN:

402458

Hom.:

90392

AF XY:

0.661

AC XY:

139725

AN XY:

211226

show subpopulations

Gnomad4 AFR exome

AF:

0.935

Gnomad4 AMR exome

AF:

0.816

Gnomad4 ASJ exome

AF:

0.739

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.821

Gnomad4 FIN exome

AF:

0.459

Gnomad4 NFE exome

AF:

0.577

Gnomad4 OTH exome

AF:

0.681

GnomAD4 genome

AF:

0.716

AC:

108822

AN:

151918

Hom.:

41246

Cov.:

AF XY:

0.718

AC XY:

53336

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.927

Gnomad4 AMR

AF:

0.789

Gnomad4 ASJ

AF:

0.737

Gnomad4 EAS

AF:

0.998

Gnomad4 SAS

AF:

0.841

Gnomad4 FIN

AF:

0.476

Gnomad4 NFE

AF:

0.577

Gnomad4 OTH

AF:

0.740

Alfa

AF:

0.639

Hom.:

4111

Bravo

AF:

0.750

Asia WGS

AF:

0.914

AC:

3175

AN:

3478

ClinVar

Significance: other; risk factor

Submissions summary: Other:7

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Crohn disease-associated growth failure, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Diabetes mellitus, type 1, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Diabetes mellitus type 2, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

INTRACRANIAL HEMORRHAGE IN BRAIN CEREBROVASCULAR MALFORMATIONS, SUSCEPTIBILITY TO

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Kaposi sarcoma

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Cholangiocarcinoma

Other:1

other, no assertion criteria provided

research

Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin

Dec 10, 2022

No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival

RHEUMATOID ARTHRITIS, SYSTEMIC JUVENILE, SUSCEPTIBILITY TO

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Benign

0.70

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.

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