rs193920884
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022163.4(MRPL46):c.289C>T(p.Arg97Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_022163.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL46 | NM_022163.4 | c.289C>T | p.Arg97Ter | stop_gained | 2/4 | ENST00000312475.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL46 | ENST00000312475.5 | c.289C>T | p.Arg97Ter | stop_gained | 2/4 | 1 | NM_022163.4 | P1 | |
MRPL46 | ENST00000558531.1 | c.289C>T | p.Arg97Ter | stop_gained | 2/2 | 2 | |||
MRPL46 | ENST00000558660.1 | n.35C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MRPL46 | ENST00000560703.1 | c.229-837C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251006Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135696
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461364Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727006
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74272
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at