GeneBe

rs2289779

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001127671.2(LIFR):​c.397+29A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LIFR
NM_001127671.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.524

Publications

14 publications found
Variant links:
Genes affected
LIFR (HGNC:6597): (LIF receptor subunit alpha) This gene encodes a protein that belongs to the type I cytokine receptor family. This protein combines with a high-affinity converter subunit, gp130, to form a receptor complex that mediates the action of the leukemia inhibitory factor, a polyfunctional cytokine that is involved in cellular differentiation, proliferation and survival in the adult and the embryo. Mutations in this gene cause Schwartz-Jampel syndrome type 2, a disease belonging to the group of the bent-bone dysplasias. A translocation that involves the promoter of this gene, t(5;8)(p13;q12) with the pleiomorphic adenoma gene 1, is associated with salivary gland pleiomorphic adenoma, a common type of benign epithelial tumor of the salivary gland. Multiple splice variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2018]
LIFR Gene-Disease associations (from GenCC):
  • Stüve-Wiedemann syndrome
    Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
  • Stüve-Wiedemann syndrome 1
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LIFRNM_001127671.2 linkc.397+29A>T intron_variant Intron 4 of 19 ENST00000453190.7 NP_001121143.1 P42702-1A8K1Z4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LIFRENST00000453190.7 linkc.397+29A>T intron_variant Intron 4 of 19 2 NM_001127671.2 ENSP00000398368.2 P42702-1
LIFRENST00000263409.8 linkc.397+29A>T intron_variant Intron 4 of 19 1 ENSP00000263409.4 P42702-1
LIFRENST00000503088.1 linkn.560+29A>T intron_variant Intron 4 of 14 1
LIFRENST00000506990.5 linkc.*49A>T downstream_gene_variant 3 ENSP00000426685.1 D6RF33

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1406260
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
698796
African (AFR)
AF:
0.00
AC:
0
AN:
32344
American (AMR)
AF:
0.00
AC:
0
AN:
40366
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25288
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38696
South Asian (SAS)
AF:
0.00
AC:
0
AN:
81946
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51702
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5570
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1072236
Other (OTH)
AF:
0.00
AC:
0
AN:
58112
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.31
DANN
Benign
0.66
PhyloP100
-0.52

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

Other links and lift over

dbSNP: rs2289779; hg19: chr5-38527228; API