1-154450143-T-TGTGTGTGTGTGTG

Variant names:

• chr1-154450143-T-TGTGTGTGTGTGTG
• rs57636717
• NM_000565.4:c.1066+163_1066+164insGTGTGTGTGTGTG

Variant summary

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

The NM_000565.4(IL6R):​c.1066+163_1066+164insGTGTGTGTGTGTG 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 0.00052 (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 rank	MANE	Protein	UniProt
IL6R	NM_000565.4	c.1066+163_1066+164insGTGTGTGTGTGTG		intron_variant	Intron 8 of 9	ENST00000368485.8	NP_000556.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL6R	ENST00000368485.8	c.1066+163_1066+164insGTGTGTGTGTGTG		intron_variant	Intron 8 of 9	1	NM_000565.4	ENSP00000357470.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 78 AN: 148610 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.000252

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000402

Gnomad ASJ AF: 0.00174

Gnomad EAS AF: 0.000586

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000289

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000744

Gnomad OTH AF: 0.00

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: 0.000525 AC: 78 AN: 148610 Hom.: 0 Cov.: 0 AF XY: 0.000579 AC XY: 42 AN XY: 72510

Gnomad4 AFR AF: 0.000252

Gnomad4 AMR AF: 0.000402

Gnomad4 ASJ AF: 0.00174

Gnomad4 EAS AF: 0.000586

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000289

Gnomad4 NFE AF: 0.000744

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00268 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;