19-38932548-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_033362.4(MRPS12):c.265C>T(p.Arg89Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,900 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R89H) has been classified as Uncertain significance.
Frequency
Consequence
NM_033362.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS12 | NM_033362.4 | c.265C>T | p.Arg89Cys | missense_variant | 3/3 | ENST00000308018.9 | |
MRPS12 | NM_021107.1 | c.265C>T | p.Arg89Cys | missense_variant | 2/2 | ||
MRPS12 | NM_033363.1 | c.265C>T | p.Arg89Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS12 | ENST00000308018.9 | c.265C>T | p.Arg89Cys | missense_variant | 3/3 | 1 | NM_033362.4 | P1 | |
MRPS12 | ENST00000402029.3 | c.265C>T | p.Arg89Cys | missense_variant | 3/3 | 1 | P1 | ||
MRPS12 | ENST00000407800.2 | c.265C>T | p.Arg89Cys | missense_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000760 AC: 19AN: 249930Hom.: 1 AF XY: 0.0000962 AC XY: 13AN XY: 135188
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1460652Hom.: 1 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 726538
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 16, 2021 | The c.265C>T (p.R89C) alteration is located in exon 3 (coding exon 2) of the MRPS12 gene. This alteration results from a C to T substitution at nucleotide position 265, causing the arginine (R) at amino acid position 89 to be replaced by a cysteine (C). 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