11-74492363-TC-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001144869.3(LIPT2):c.467delG(p.Gly156GlufsTer40) variant causes a frameshift, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,118 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144869.3 frameshift, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.467delG | p.Gly156GlufsTer40 | frameshift_variant, splice_region_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.505delG | p.Glu169SerfsTer24 | frameshift_variant, splice_region_variant | Exon 2 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.238delG | p.Glu80SerfsTer24 | frameshift_variant, splice_region_variant | Exon 2 of 2 | NP_001316871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT2 | ENST00000310109.5 | c.467delG | p.Gly156GlufsTer40 | frameshift_variant, splice_region_variant | Exon 2 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2 | ENST00000527115.1 | c.115delG | p.Glu39fs | frameshift_variant, splice_region_variant | Exon 2 of 2 | 2 | ENSP00000431210.1 | |||
LIPT2 | ENST00000528085.1 | c.181delG | p.Glu61fs | frameshift_variant, splice_region_variant | Exon 2 of 2 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74316
ClinVar
Submissions by phenotype
not provided Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with LIPT2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly156Glufs*40) in the LIPT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 76 amino acid(s) of the LIPT2 protein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at