16-48261571-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031490.5(LONP2):c.871G>A(p.Val291Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000474 in 1,583,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031490.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LONP2 | NM_031490.5 | c.871G>A | p.Val291Ile | missense_variant | 5/15 | ENST00000285737.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LONP2 | ENST00000285737.9 | c.871G>A | p.Val291Ile | missense_variant | 5/15 | 1 | NM_031490.5 | P1 | |
LONP2 | ENST00000535754.5 | c.739G>A | p.Val247Ile | missense_variant | 4/14 | 1 | |||
LONP2 | ENST00000416006.7 | c.739G>A | p.Val247Ile | missense_variant, NMD_transcript_variant | 4/13 | 2 | |||
LONP2 | ENST00000566755.5 | c.871G>A | p.Val291Ile | missense_variant, NMD_transcript_variant | 5/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000268 AC: 4AN: 149326Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000258 AC: 6AN: 232914Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126340
GnomAD4 exome AF: 0.0000495 AC: 71AN: 1433948Hom.: 0 Cov.: 30 AF XY: 0.0000407 AC XY: 29AN XY: 713190
GnomAD4 genome ? AF: 0.0000268 AC: 4AN: 149326Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72642
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.871G>A (p.V291I) alteration is located in exon 5 (coding exon 5) of the LONP2 gene. This alteration results from a G to A substitution at nucleotide position 871, causing the valine (V) at amino acid position 291 to be replaced by an isoleucine (I). 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