11-74492263-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001144869.3(LIPT2):c.568A>T(p.Thr190Ser) variant causes a missense change. The variant allele was found at a frequency of 0.608 in 1,551,212 control chromosomes in the GnomAD database, including 289,463 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.568A>T | p.Thr190Ser | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.606A>T | p.Gly202Gly | synonymous_variant | Exon 2 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.339A>T | p.Gly113Gly | synonymous_variant | Exon 2 of 2 | NP_001316871.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.553 AC: 83885AN: 151820Hom.: 23924 Cov.: 31
GnomAD3 exomes AF: 0.580 AC: 90980AN: 156780Hom.: 26820 AF XY: 0.581 AC XY: 48249AN XY: 83056
GnomAD4 exome AF: 0.614 AC: 858739AN: 1399276Hom.: 265550 Cov.: 49 AF XY: 0.612 AC XY: 422601AN XY: 690142
GnomAD4 genome AF: 0.552 AC: 83900AN: 151936Hom.: 23913 Cov.: 31 AF XY: 0.547 AC XY: 40604AN XY: 74272
ClinVar
Submissions by phenotype
not provided Benign:3
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Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities Benign:1
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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