9-135501025-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016034.5(MRPS2):c.71G>A(p.Gly24Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000844 in 1,611,614 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_016034.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS2 | NM_016034.5 | c.71G>A | p.Gly24Asp | missense_variant | 2/4 | ENST00000241600.10 | NP_057118.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS2 | ENST00000241600.10 | c.71G>A | p.Gly24Asp | missense_variant | 2/4 | 1 | NM_016034.5 | ENSP00000241600 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152080Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000622 AC: 15AN: 241150Hom.: 0 AF XY: 0.0000679 AC XY: 9AN XY: 132560
GnomAD4 exome AF: 0.0000808 AC: 118AN: 1459534Hom.: 1 Cov.: 30 AF XY: 0.0000785 AC XY: 57AN XY: 726076
GnomAD4 genome AF: 0.000118 AC: 18AN: 152080Hom.: 0 Cov.: 33 AF XY: 0.0000943 AC XY: 7AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2024 | The c.71G>A (p.G24D) alteration is located in exon 2 (coding exon 2) of the MRPS2 gene. This alteration results from a G to A substitution at nucleotide position 71, causing the glycine (G) at amino acid position 24 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 23, 2023 | This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 24 of the MRPS2 protein (p.Gly24Asp). This variant is present in population databases (rs138860958, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with MRPS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2197872). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The aspartic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at