rs2298885

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000641.4(IL11):​c.*1135G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,134 control chromosomes in the GnomAD database, including 5,765 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 0.27 ( 5764 hom., cov: 32)
Exomes 𝑓: 0.30 ( 1 hom. )

Consequence

IL11
NM_000641.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL11NM_000641.4 linkuse as main transcriptc.*1135G>A 3_prime_UTR_variant 5/5 ENST00000264563.7
IL11NM_001267718.2 linkuse as main transcriptc.*1135G>A 3_prime_UTR_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL11ENST00000264563.7 linkuse as main transcriptc.*1135G>A 3_prime_UTR_variant 5/51 NM_000641.4 P1P20809-1

Frequencies

GnomAD3 genomes
AF:
0.267
AC:
40660
AN:
152006
Hom.:
5757
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.206
Gnomad AMI
AF:
0.200
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.331
Gnomad EAS
AF:
0.157
Gnomad SAS
AF:
0.410
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.351
Gnomad NFE
AF:
0.317
Gnomad OTH
AF:
0.274
GnomAD4 exome
AF:
0.300
AC:
3
AN:
10
Hom.:
1
Cov.:
0
AF XY:
0.300
AC XY:
3
AN XY:
10
show subpopulations
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.375
GnomAD4 genome
AF:
0.267
AC:
40681
AN:
152124
Hom.:
5764
Cov.:
32
AF XY:
0.264
AC XY:
19660
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.206
Gnomad4 AMR
AF:
0.234
Gnomad4 ASJ
AF:
0.331
Gnomad4 EAS
AF:
0.157
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.317
Gnomad4 OTH
AF:
0.271
Alfa
AF:
0.312
Hom.:
9580
Bravo
AF:
0.262
Asia WGS
AF:
0.278
AC:
964
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.5
DANN
Benign
0.45

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

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

Other links and lift over

dbSNP: rs2298885; hg19: chr19-55876240; COSMIC: COSV52773661; COSMIC: COSV52773661; API