15-88467221-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022163.4(MRPL46):c.157C>G(p.Leu53Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000768 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022163.4 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 |
---|---|---|---|---|---|---|---|
MRPL46 | NM_022163.4 | c.157C>G | p.Leu53Val | missense_variant | 1/4 | ENST00000312475.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL46 | ENST00000312475.5 | c.157C>G | p.Leu53Val | missense_variant | 1/4 | 1 | NM_022163.4 | P1 | |
MRPL46 | ENST00000558531.1 | c.157C>G | p.Leu53Val | missense_variant | 1/2 | 2 | |||
MRPL46 | ENST00000560703.1 | c.157C>G | p.Leu53Val | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251098Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135780
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.0000715 AC XY: 52AN XY: 727178
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2021 | The c.157C>G (p.L53V) alteration is located in exon 1 (coding exon 1) of the MRPL46 gene. This alteration results from a C to G substitution at nucleotide position 157, causing the leucine (L) at amino acid position 53 to be replaced by a valine (V). 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