rs964306396
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_023936.2(MRPS34):c.251C>T(p.Ser84Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,453,386 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023936.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS34 | NM_023936.2 | c.251C>T | p.Ser84Phe | missense_variant | Exon 1 of 3 | ENST00000397375.7 | NP_076425.1 | |
EME2 | NM_001257370.2 | c.-359G>A | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000568449.7 | NP_001244299.1 | ||
MRPS34 | NM_001300900.2 | c.251C>T | p.Ser84Phe | missense_variant | Exon 1 of 3 | NP_001287829.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS34 | ENST00000397375.7 | c.251C>T | p.Ser84Phe | missense_variant | Exon 1 of 3 | 1 | NM_023936.2 | ENSP00000380531.3 | ||
MRPS34 | ENST00000177742.7 | c.251C>T | p.Ser84Phe | missense_variant | Exon 1 of 3 | 1 | ENSP00000177742.3 | |||
EME2 | ENST00000568449 | c.-359G>A | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_001257370.2 | ENSP00000457353.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152252Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000159 AC: 1AN: 62884Hom.: 0 AF XY: 0.0000299 AC XY: 1AN XY: 33486
GnomAD4 exome AF: 0.0000123 AC: 16AN: 1301134Hom.: 0 Cov.: 63 AF XY: 0.00000787 AC XY: 5AN XY: 635006
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152252Hom.: 0 Cov.: 35 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 84 of the MRPS34 protein (p.Ser84Phe). This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with MRPS34-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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