Variant 7-22726814-T-A 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.54-109A>T 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 0.696 in 156,484 control chromosomes in the GnomAD database, including 39,121 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 0.70 ( 37987 hom., cov: 31)

Exomes 𝑓: 0.61 ( 1134 hom. )

Consequence

IL6-AS1
NR_131935.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243

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:

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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 = 0.975 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.54-109A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Appris
IL6-AS1	ENST00000325042.2 linkuse as main transcript	n.54-109A>T	intron_variant, non_coding_transcript_variant	1
IL6	ENST00000404625.5 linkuse as main transcript	c.-84-365T>A	intron_variant	5	P1
STEAP1B	ENST00000650428.1 linkuse as main transcript	n.46+754A>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

105171

AN:

150516

Hom.:

37941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.654

Gnomad AMR

AF:

0.784

Gnomad ASJ

AF:

0.737

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.847

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.811

Gnomad NFE

AF:

0.590

Gnomad OTH

AF:

0.734

GnomAD4 exome

AF:

0.613

AC:

3595

AN:

5860

Hom.:

1134

AF XY:

0.614

AC XY:

1863

AN XY:

3036

show subpopulations

Gnomad4 AFR exome

AF:

0.819

Gnomad4 AMR exome

AF:

0.799

Gnomad4 ASJ exome

AF:

0.736

Gnomad4 EAS exome

AF:

0.991

Gnomad4 SAS exome

AF:

0.880

Gnomad4 FIN exome

AF:

0.452

Gnomad4 NFE exome

AF:

0.549

Gnomad4 OTH exome

AF:

0.632

GnomAD4 genome

AF:

0.699

AC:

105271

AN:

150624

Hom.:

37987

Cov.:

AF XY:

0.702

AC XY:

51664

AN XY:

73594

show subpopulations

Gnomad4 AFR

AF:

0.840

Gnomad4 AMR

AF:

0.784

Gnomad4 ASJ

AF:

0.737

Gnomad4 EAS

AF:

0.997

Gnomad4 SAS

AF:

0.848

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.590

Gnomad4 OTH

AF:

0.737

Alfa

AF:

0.621

Hom.:

3544

Bravo

AF:

0.724

Asia WGS

AF:

0.902

AC:

3133

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

8.8

DANN

Benign

0.21

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

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