11-74493434-G-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001144869.3(LIPT2):c.270C>A(p.Thr90Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000653 in 1,505,074 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001144869.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.270C>A | p.Thr90Thr | synonymous_variant | Exon 1 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.270C>A | p.Thr90Thr | synonymous_variant | Exon 1 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.237+33C>A | intron_variant | Intron 1 of 1 | NP_001316871.1 | |||
LIPT2-AS1 | NR_171028.1 | n.55G>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.270C>A | p.Thr90Thr | synonymous_variant | Exon 1 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2-AS1 | ENST00000526036.1 | n.69G>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
LIPT2 | ENST00000528085.1 | c.180+33C>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.00348 AC: 530AN: 152204Hom.: 3 Cov.: 34
GnomAD3 exomes AF: 0.000229 AC: 23AN: 100328Hom.: 0 AF XY: 0.000196 AC XY: 11AN XY: 56028
GnomAD4 exome AF: 0.000335 AC: 453AN: 1352758Hom.: 1 Cov.: 43 AF XY: 0.000253 AC XY: 169AN XY: 666948
GnomAD4 genome AF: 0.00348 AC: 530AN: 152316Hom.: 3 Cov.: 34 AF XY: 0.00330 AC XY: 246AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:2
- -
ENSG00000254837: BS1, BS2; LIPT2: BP4, BP7, BS1, BS2 -
LIPT2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at