1-175014763-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_022100.3(MRPS14):c.293G>A(p.Arg98His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,032 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. R98C) has been classified as Uncertain significance.
Frequency
Consequence
NM_022100.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS14 | ENST00000476371.1 | c.293G>A | p.Arg98His | missense_variant | Exon 3 of 3 | 1 | NM_022100.3 | ENSP00000420714.1 | ||
MRPS14 | ENST00000367677.3 | n.*202G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | ENSP00000431220.1 | ||||
MRPS14 | ENST00000367677.3 | n.*202G>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000431220.1 | ||||
MRPS14 | ENST00000498253.1 | n.62G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251158Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135812
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727244
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74318
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 98 of the MRPS14 protein (p.Arg98His). This variant is present in population databases (rs149343934, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with MRPS14-related conditions. ClinVar contains an entry for this variant (Variation ID: 2892030). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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