11-74493453-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001144869.3(LIPT2):āc.251G>Cā(p.Gly84Ala) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.251G>C | p.Gly84Ala | missense_variant | Exon 1 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.251G>C | p.Gly84Ala | missense_variant | Exon 1 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.237+14G>C | intron_variant | Intron 1 of 1 | NP_001316871.1 | |||
LIPT2-AS1 | NR_171028.1 | n.74C>G | 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.251G>C | p.Gly84Ala | missense_variant | Exon 1 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2-AS1 | ENST00000526036.1 | n.88C>G | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
LIPT2 | ENST00000528085.1 | c.180+14G>C | intron_variant | Intron 1 of 1 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1339750Hom.: 0 Cov.: 43 AF XY: 0.00 AC XY: 0AN XY: 660250
GnomAD4 genome Cov.: 34
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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 1715038). 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 replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 84 of the LIPT2 protein (p.Gly84Ala). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at