11-74493427-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001144869.3(LIPT2):c.277G>A(p.Gly93Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,354,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144869.3 missense
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.277G>A | p.Gly93Ser | missense_variant | Exon 1 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.277G>A | p.Gly93Ser | missense_variant | Exon 1 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.237+40G>A | intron_variant | Intron 1 of 1 | NP_001316871.1 | |||
LIPT2-AS1 | NR_171028.1 | n.48C>T | 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.277G>A | p.Gly93Ser | missense_variant | Exon 1 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2-AS1 | ENST00000526036.1 | n.62C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
LIPT2 | ENST00000528085.1 | c.180+40G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.0000192 AC: 26AN: 1354738Hom.: 0 Cov.: 43 AF XY: 0.0000180 AC XY: 12AN XY: 667962
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.277G>A (p.G93S) alteration is located in exon 1 (coding exon 1) of the LIPT2 gene. This alteration results from a G to A substitution at nucleotide position 277, causing the glycine (G) at amino acid position 93 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at