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rs1800795

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: đť‘“ 0.72 ( 41246 hom., cov: 29)
Exomes đť‘“: 0.65 ( 90392 hom. )

Consequence

IL6-AS1
NR_131935.1 intron, non_coding_transcript

Scores

2

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 (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]

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-AS1NR_131935.1 linkuse as main transcriptn.54-321G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL6-AS1ENST00000325042.2 linkuse as main transcriptn.54-321G>C intron_variant, non_coding_transcript_variant 1
IL6ENST00000404625.5 linkuse as main transcriptc.-84-153C>G intron_variant 5 P1
STEAP1BENST00000650428.1 linkuse as main transcriptn.46+542G>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.716
AC:
108695
AN:
151800
Hom.:
41177
Cov.:
29
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.:
29
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 providedliterature onlyOMIMSep 01, 2007- -
Diabetes mellitus, type 1, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMSep 01, 2007- -
Diabetes mellitus type 2, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMSep 01, 2007- -
INTRACRANIAL HEMORRHAGE IN BRAIN CEREBROVASCULAR MALFORMATIONS, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria providedliterature onlyOMIMSep 01, 2007- -
Kaposi sarcoma Other:1
risk factor, no assertion criteria providedliterature onlyOMIMSep 01, 2007- -
Cholangiocarcinoma Other:1
other, no assertion criteria providedresearchDepartment of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin BerlinDec 10, 2022No 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 providedliterature onlyOMIMSep 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1800795; hg19: chr7-22766645; API