11-74493441-AGGCCACCGC-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001144869.3(LIPT2):c.254_262delGCGGTGGCC(p.Arg85_Gly87del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000657 in 152,186 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144869.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.254_262delGCGGTGGCC | p.Arg85_Gly87del | disruptive_inframe_deletion | Exon 1 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.254_262delGCGGTGGCC | p.Arg85_Gly87del | disruptive_inframe_deletion | Exon 1 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.237+17_237+25delGCGGTGGCC | intron_variant | Intron 1 of 1 | NP_001316871.1 | |||
LIPT2-AS1 | NR_171028.1 | n.67_75delACCGCGGCC | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT2 | ENST00000310109.5 | c.254_262delGCGGTGGCC | p.Arg85_Gly87del | disruptive_inframe_deletion | Exon 1 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2-AS1 | ENST00000526036.1 | n.81_89delACCGCGGCC | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
LIPT2 | ENST00000528085.1 | c.180+17_180+25delGCGGTGGCC | intron_variant | Intron 1 of 1 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 34
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.254_262del, results in the deletion of 3 amino acid(s) of the LIPT2 protein (p.Arg85_Gly87del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LIPT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2011276). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at