chr5-38475553-T-TTAA
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001127671.2(LIFR):c.*6041_*6042insTTA variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.000111 in 189,952 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
LIFR
NM_001127671.2 3_prime_UTR
NM_001127671.2 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.64
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| LIFR | NM_001127671.2 | c.*6041_*6042insTTA | 3_prime_UTR_variant | 20/20 | ENST00000453190.7 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LIFR | ENST00000453190.7 | c.*6041_*6042insTTA | 3_prime_UTR_variant | 20/20 | 2 | NM_001127671.2 | P1 | ||
| LIFR | ENST00000263409.8 | c.*6041_*6042insTTA | 3_prime_UTR_variant | 20/20 | 1 | P1 |
Frequencies
GnomAD3 genomes 0.000105 AC: 16AN: 152106Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000133 AC: 5AN: 37728Hom.: 0 Cov.: 0 AF XY: 0.0000570 AC XY: 1AN XY: 17550
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GnomAD4 genome 0.000105 AC: 16AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74432
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Stuve-Wiedemann syndrome Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at