rs780263579
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_023936.2(MRPS34):c.514G>A(p.Ala172Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,840 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 (★).
Frequency
Consequence
NM_023936.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS34 | ENST00000397375.7 | c.514G>A | p.Ala172Thr | missense_variant | Exon 3 of 3 | 1 | NM_023936.2 | ENSP00000380531.3 | ||
MRPS34 | ENST00000177742.7 | c.535G>A | p.Ala179Thr | missense_variant | Exon 3 of 3 | 1 | ENSP00000177742.3 | |||
MRPS34 | ENST00000569585.1 | n.245G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250048Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135634
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460608Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726594
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.514G>A (p.A172T) alteration is located in exon 3 (coding exon 3) of the MRPS34 gene. This alteration results from a G to A substitution at nucleotide position 514, causing the alanine (A) at amino acid position 172 to be replaced by a threonine (T). 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