7-22727026-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: other; risk factor no assertion criteria provided O:7
• Conservation: PhyloP100: 3.25

Genes affected

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

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]

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]

ACMG classification

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	n.54-321G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL6-AS1	ENST00000325042.2	n.54-321G>C		intron_variant, non_coding_transcript_variant		1
IL6	ENST00000404625.5	c.-84-153C>G		intron_variant		5		P1
STEAP1B	ENST00000650428.1	n.46+542G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108695 AN: 151800 Hom.: 41177 Cov.: 29

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

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.: 29 AF XY: 0.718 AC XY: 53336 AN XY: 74234

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

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	16
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

Other links and lift over

dbSNP: rs1800795; hg19: chr7-22766645;