11-74492224-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144869.3(LIPT2):āc.607G>Cā(p.Val203Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.607G>C | p.Val203Leu | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.*21G>C | 3_prime_UTR_variant | Exon 2 of 2 | NP_001316870.1 | |||
LIPT2 | NM_001329942.2 | c.*21G>C | 3_prime_UTR_variant | Exon 2 of 2 | NP_001316871.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1399428Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 690218
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at