1-36456246-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_031280.4(MRPS15):c.577C>T(p.Pro193Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,840 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P193L) has been classified as Uncertain significance.
Frequency
Consequence
NM_031280.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS15 | NM_031280.4 | c.577C>T | p.Pro193Ser | missense_variant | 7/8 | ENST00000373116.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS15 | ENST00000373116.6 | c.577C>T | p.Pro193Ser | missense_variant | 7/8 | 1 | NM_031280.4 | P1 | |
MRPS15 | ENST00000462067.1 | n.1401C>T | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
MRPS15 | ENST00000477040.1 | n.321C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MRPS15 | ENST00000488606.5 | n.1914C>T | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251192Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135754
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461800Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727200
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.577C>T (p.P193S) alteration is located in exon 7 (coding exon 7) of the MRPS15 gene. This alteration results from a C to T substitution at nucleotide position 577, causing the proline (P) at amino acid position 193 to be replaced by a serine (S). 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