chr3-15065131-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022497.5(MRPS25):c.64G>A(p.Val22Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,609,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022497.5 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 |
---|---|---|---|---|---|---|---|
MRPS25 | NM_022497.5 | c.64G>A | p.Val22Met | missense_variant | 1/4 | ENST00000253686.7 | |
MRPS25 | NR_135246.2 | n.185G>A | non_coding_transcript_exon_variant | 1/5 | |||
MRPS25 | NR_135247.2 | n.185G>A | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS25 | ENST00000253686.7 | c.64G>A | p.Val22Met | missense_variant | 1/4 | 1 | NM_022497.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000629 AC: 15AN: 238554Hom.: 0 AF XY: 0.0000696 AC XY: 9AN XY: 129232
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1456862Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 724242
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.64G>A (p.V22M) alteration is located in exon 1 (coding exon 1) of the MRPS25 gene. This alteration results from a G to A substitution at nucleotide position 64, causing the valine (V) at amino acid position 22 to be replaced by a methionine (M). 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