15-88465689-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022163.4(MRPL46):c.313C>T(p.Leu105Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL46 | NM_022163.4 | c.313C>T | p.Leu105Phe | missense_variant | 2/4 | ENST00000312475.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL46 | ENST00000312475.5 | c.313C>T | p.Leu105Phe | missense_variant | 2/4 | 1 | NM_022163.4 | P1 | |
MRPL46 | ENST00000558531.1 | c.313C>T | p.Leu105Phe | missense_variant | 2/2 | 2 | |||
MRPL46 | ENST00000558660.1 | n.59C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MRPL46 | ENST00000560703.1 | c.229-813C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251348Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135850
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461714Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727156
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.313C>T (p.L105F) alteration is located in exon 2 (coding exon 2) of the MRPL46 gene. This alteration results from a C to T substitution at nucleotide position 313, causing the leucine (L) at amino acid position 105 to be replaced by a phenylalanine (F). 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