8-120432099-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_014078.6(MRPL13):āc.176T>Cā(p.Ile59Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000935 in 1,604,236 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 (ā ).
Frequency
Consequence
NM_014078.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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 |
---|---|---|---|---|---|---|---|---|---|---|
MRPL13 | ENST00000306185.8 | c.176T>C | p.Ile59Thr | missense_variant | Exon 3 of 7 | 1 | NM_014078.6 | ENSP00000306548.3 | ||
MRPL13 | ENST00000518696.5 | n.152-6733T>C | intron_variant | Intron 2 of 5 | 1 | ENSP00000428867.1 | ||||
MRPL13 | ENST00000518918.1 | c.104T>C | p.Ile35Thr | missense_variant | Exon 3 of 6 | 2 | ENSP00000430545.1 | |||
MRPL13 | ENST00000520677.1 | n.157-6733T>C | intron_variant | Intron 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000247 AC: 6AN: 242724Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131176
GnomAD4 exome AF: 0.00000964 AC: 14AN: 1452172Hom.: 0 Cov.: 29 AF XY: 0.00000554 AC XY: 4AN XY: 722104
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.176T>C (p.I59T) alteration is located in exon 3 (coding exon 3) of the MRPL13 gene. This alteration results from a T to C substitution at nucleotide position 176, causing the isoleucine (I) at amino acid position 59 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