rs7802307

Variant names:

• chr7-22726814-T-A
• rs7802307
• ENST00000325042.2:n.54-109A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-22726814-T-A
• chr7-22726814-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000325042.2(IL6-AS1):​n.54-109A>T variant causes a intron 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 ENST00000325042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000325042.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL6-AS1	NR_131935.1		n.54-109A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL6-AS1	ENST00000325042.2	TSL:1	n.54-109A>T		intron	N/A
	IL6	ENST00000404625.5	TSL:5	c.-84-365T>A		intron	N/A	ENSP00000385675.1	P05231
	STEAP1B	ENST00000650428.1		n.46+754A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 105171 AN: 150516 Hom.: 37941 Cov.: 31

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

African (AFR) AF: 0.819 AC: 149 AN: 182

American (AMR) AF: 0.799 AC: 366 AN: 458

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 131 AN: 178

East Asian (EAS) AF: 0.991 AC: 222 AN: 224

South Asian (SAS) AF: 0.880 AC: 183 AN: 208

European-Finnish (FIN) AF: 0.452 AC: 104 AN: 230

Middle Eastern (MID) AF: 0.821 AC: 23 AN: 28

European-Non Finnish (NFE) AF: 0.549 AC: 2201 AN: 4010

Other (OTH) AF: 0.632 AC: 216 AN: 342

GnomAD4 genome AF: 0.699 AC: 105271 AN: 150624 Hom.: 37987 Cov.: 31 AF XY: 0.702 AC XY: 51664 AN XY: 73594

African (AFR) AF: 0.840 AC: 34376 AN: 40916

American (AMR) AF: 0.784 AC: 11914 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2550 AN: 3460

East Asian (EAS) AF: 0.997 AC: 5131 AN: 5144

South Asian (SAS) AF: 0.848 AC: 4050 AN: 4776

European-Finnish (FIN) AF: 0.489 AC: 5049 AN: 10326

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 39832 AN: 67522

Other (OTH) AF: 0.737 AC: 1538 AN: 2088

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.21
PhyloP100		-0.24
PromoterAI		0.0018	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7802307; hg19: chr7-22766433;