rs1042506

Variant names:

• chr19-55365743-A-C
• rs1042506
• NM_000641.4:c.*264T>G

Variant summary

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

The NM_000641.4(IL11):​c.*264T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 500,052 control chromosomes in the GnomAD database, including 4,328 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 0.13 (1345 hom., cov: 30)
  • Exomes 𝑓: 0.12 (2983 hom.)
• Consequence: IL11 NM_000641.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 13 publications found

Genes affected

IL11 (HGNC:5966): (interleukin 11) The protein encoded by this gene is a member of the gp130 family of cytokines. These cytokines drive the assembly of multisubunit receptor complexes, all of which contain at least one molecule of the transmembrane signaling receptor IL6ST (gp130). This cytokine is shown to stimulate the T-cell-dependent development of immunoglobulin-producing B cells. It is also found to support the proliferation of hematopoietic stem cells and megakaryocyte progenitor cells. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jun 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000641.4. 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
	IL11	NM_000641.4	MANE Select	c.*264T>G		3_prime_UTR	Exon 5 of 5	NP_000632.1	A8K3F7
	IL11	NM_001267718.2		c.*264T>G		3_prime_UTR	Exon 4 of 4	NP_001254647.1	P20809-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL11	ENST00000264563.7	TSL:1 MANE Select	c.*264T>G		3_prime_UTR	Exon 5 of 5	ENSP00000264563.1	P20809-1
	IL11	ENST00000585513.1	TSL:1	c.*264T>G		3_prime_UTR	Exon 5 of 5	ENSP00000467355.1	P20809-1
	IL11	ENST00000590625.5	TSL:2	c.*264T>G		3_prime_UTR	Exon 4 of 4	ENSP00000465705.1	P20809-2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19463 AN: 151764 Hom.: 1342 Cov.: 30

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0852

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00581

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.123 AC: 42801 AN: 348170 Hom.: 2983 Cov.: 3 AF XY: 0.119 AC XY: 21854 AN XY: 184240

African (AFR) AF: 0.125 AC: 914 AN: 7326

American (AMR) AF: 0.0844 AC: 846 AN: 10022

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 1206 AN: 10796

East Asian (EAS) AF: 0.00307 AC: 61 AN: 19900

South Asian (SAS) AF: 0.0733 AC: 2780 AN: 37946

European-Finnish (FIN) AF: 0.179 AC: 4067 AN: 22742

Middle Eastern (MID) AF: 0.0793 AC: 128 AN: 1614

European-Non Finnish (NFE) AF: 0.140 AC: 30340 AN: 217426

Other (OTH) AF: 0.121 AC: 2459 AN: 20398

GnomAD4 genome AF: 0.128 AC: 19481 AN: 151882 Hom.: 1345 Cov.: 30 AF XY: 0.128 AC XY: 9503 AN XY: 74206

African (AFR) AF: 0.127 AC: 5254 AN: 41390

American (AMR) AF: 0.0849 AC: 1297 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3466

East Asian (EAS) AF: 0.00622 AC: 32 AN: 5148

South Asian (SAS) AF: 0.0729 AC: 351 AN: 4816

European-Finnish (FIN) AF: 0.193 AC: 2039 AN: 10556

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9704 AN: 67928

Other (OTH) AF: 0.124 AC: 261 AN: 2108

Alfa AF: 0.135 Hom.: 1356

Bravo AF: 0.123

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		1.1
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1042506;

hg19: chr19-55877111;