rs749922789
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5
The NM_018116.4(MSTO1):c.1033C>T(p.Arg345Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,462 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R345H) has been classified as Uncertain significance.
Frequency
Consequence
NM_018116.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTO1 | NM_018116.4 | c.1033C>T | p.Arg345Cys | missense_variant | 10/14 | ENST00000245564.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.1033C>T | p.Arg345Cys | missense_variant | 10/14 | 1 | NM_018116.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152222Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251046Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135680
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461240Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 726982
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152222Hom.: 0 Cov.: 30 AF XY: 0.0000672 AC XY: 5AN XY: 74364
ClinVar
Submissions by phenotype
Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 22, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at