11-74492141-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001144869.3(LIPT2):c.690C>T(p.Pro230Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 1,550,706 control chromosomes in the GnomAD database, including 140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001144869.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.690C>T | p.Pro230Pro | synonymous_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.*104C>T | 3_prime_UTR_variant | Exon 2 of 2 | NP_001316870.1 | |||
LIPT2 | NM_001329942.2 | c.*104C>T | 3_prime_UTR_variant | Exon 2 of 2 | NP_001316871.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00464 AC: 706AN: 152100Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.0117 AC: 1836AN: 156400Hom.: 86 AF XY: 0.00882 AC XY: 731AN XY: 82884
GnomAD4 exome AF: 0.00199 AC: 2780AN: 1398488Hom.: 121 Cov.: 30 AF XY: 0.00164 AC XY: 1133AN XY: 689806
GnomAD4 genome AF: 0.00468 AC: 712AN: 152218Hom.: 19 Cov.: 32 AF XY: 0.00566 AC XY: 421AN XY: 74412
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