rs6875155

Variant names:

• chr5-55975226-G-A
• rs6875155
• NM_002184.4:c.64+989C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-55975226-G-A
• chr5-55975226-G-C

Variant summary

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

The NM_002184.4(IL6ST):​c.64+989C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,048 control chromosomes in the GnomAD database, including 1,127 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 0.12 (1127 hom., cov: 31)
• Consequence: IL6ST NM_002184.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 6 publications found

Genes affected

IL6ST (HGNC:6021): (interleukin 6 cytokine family signal transducer) The protein encoded by this gene is a signal transducer shared by many cytokines, including interleukin 6 (IL6), ciliary neurotrophic factor (CNTF), leukemia inhibitory factor (LIF), and oncostatin M (OSM). This protein functions as a part of the cytokine receptor complex. The activation of this protein is dependent upon the binding of cytokines to their receptors. vIL6, a protein related to IL6 and encoded by the Kaposi sarcoma-associated herpesvirus, can bypass the interleukin 6 receptor (IL6R) and directly activate this protein. Knockout studies in mice suggest that this gene plays a critical role in regulating myocyte apoptosis. Alternatively spliced transcript variants have been described. A related pseudogene has been identified on chromosome 17. [provided by RefSeq, May 2014]

IL6ST Gene-Disease associations (from GenCC):

• hyper-IgE recurrent infection syndrome 4A, autosomal dominant

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• hyper-IgE recurrent infection syndrome 4, autosomal recessive

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002184.4. 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
	IL6ST	NM_002184.4	MANE Select	c.64+989C>T		intron	N/A	NP_002175.2
	IL6ST	NM_001364275.2		c.64+989C>T		intron	N/A	NP_001351204.1	A0A0A0N0L5
	IL6ST	NM_001190981.2		c.64+989C>T		intron	N/A	NP_001177910.1	P40189-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL6ST	ENST00000381298.7	TSL:1 MANE Select	c.64+989C>T		intron	N/A	ENSP00000370698.2	P40189-1
	IL6ST	ENST00000381294.8	TSL:1	c.64+989C>T		intron	N/A	ENSP00000370694.3	P40189-3
	IL6ST	ENST00000522633.2	TSL:1	c.64+989C>T		intron	N/A	ENSP00000435399.1	P40189-2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17857 AN: 151930 Hom.: 1126 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.117 AC: 17863 AN: 152048 Hom.: 1127 Cov.: 31 AF XY: 0.115 AC XY: 8512 AN XY: 74306

African (AFR) AF: 0.130 AC: 5382 AN: 41450

American (AMR) AF: 0.0990 AC: 1512 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.0327 AC: 169 AN: 5170

South Asian (SAS) AF: 0.0697 AC: 336 AN: 4818

European-Finnish (FIN) AF: 0.133 AC: 1408 AN: 10566

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8095 AN: 67986

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.101 Hom.: 407

Bravo AF: 0.118

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.66
PhyloP100		0.25
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: rs6875155; hg19: chr5-55271054;