rs57636717

chr1-154450143-T-TGchr1-154450143-T-TGTGchr1-154450143-T-TGTGTGchr1-154450143-T-TGTGTGTGchr1-154450143-T-TGTGTGTGTGchr1-154450143-T-TGTGTGTGTGTGchr1-154450143-T-TGTGTGTGTGTGTGchr1-154450143-T-TGTGTGTGTGTGTGTGchr1-154450143-T-TGTGTGTGTGTGTGTGTGchr1-154450143-T-TGTGTGTGTGTGTGTGTGTGchr1-154450143-T-TGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000565.4(IL6R):c.1066+163_1066+164insG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00082 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: IL6R NM_000565.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508

Genes affected

IL6R (HGNC:6019): (interleukin 6 receptor) This gene encodes a subunit of the interleukin 6 (IL6) receptor complex. Interleukin 6 is a potent pleiotropic cytokine that regulates cell growth and differentiation and plays an important role in the immune response. The IL6 receptor is a protein complex consisting of this protein and interleukin 6 signal transducer (IL6ST/GP130/IL6-beta), a receptor subunit also shared by many other cytokines. Dysregulated production of IL6 and this receptor are implicated in the pathogenesis of many diseases, such as multiple myeloma, autoimmune diseases and prostate cancer. Alternatively spliced transcript variants encoding distinct isoforms have been identified in this gene. A pseudogene of this gene is found on chromosome 9. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL6R	NM_000565.4	c.1066+163_1066+164insG		intron_variant		ENST00000368485.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL6R	ENST00000368485.8	c.1066+163_1066+164insG		intron_variant		1	NM_000565.4	P1
IL6R	ENST00000344086.8	c.1066+163_1066+164insG		intron_variant		1
IL6R	ENST00000515190.1	c.474+163_474+164insG		intron_variant		2
IL6R	ENST00000507256.1	n.264+163_264+164insG		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 121 AN: 148530 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.000480

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000537

Gnomad ASJ AF: 0.000582

Gnomad EAS AF: 0.000587

Gnomad SAS AF: 0.000424

Gnomad FIN AF: 0.000674

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00118

Gnomad OTH AF: 0.000491

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000821 AC: 122 AN: 148638 Hom.: 0 Cov.: 0 AF XY: 0.000757 AC XY: 55 AN XY: 72610

Gnomad4 AFR AF: 0.000478

Gnomad4 AMR AF: 0.000603

Gnomad4 ASJ AF: 0.000582

Gnomad4 EAS AF: 0.000588

Gnomad4 SAS AF: 0.000424

Gnomad4 FIN AF: 0.000674

Gnomad4 NFE AF: 0.00118

Gnomad4 OTH AF: 0.000485

Alfa AF: 0.00268 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs57636717; hg19: chr1-154422619;