NM_001144869.3:c.613G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144869.3(LIPT2):c.613G>A(p.Val205Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000902 in 1,551,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.613G>A | p.Val205Met | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.*27G>A | 3_prime_UTR_variant | Exon 2 of 2 | NP_001316870.1 | |||
LIPT2 | NM_001329942.2 | c.*27G>A | 3_prime_UTR_variant | Exon 2 of 2 | NP_001316871.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156638Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83012
GnomAD4 exome AF: 0.00000643 AC: 9AN: 1399420Hom.: 0 Cov.: 30 AF XY: 0.00000869 AC XY: 6AN XY: 690218
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.613G>A (p.V205M) alteration is located in exon 2 (coding exon 2) of the LIPT2 gene. This alteration results from a G to A substitution at nucleotide position 613, causing the valine (V) at amino acid position 205 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at