13-41252973-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004294.4(MTRF1):c.565G>A(p.Val189Met) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004294.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTRF1 | NM_004294.4 | c.565G>A | p.Val189Met | missense_variant | Exon 4 of 10 | ENST00000379480.9 | NP_004285.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTRF1 | ENST00000379480.9 | c.565G>A | p.Val189Met | missense_variant | Exon 4 of 10 | 1 | NM_004294.4 | ENSP00000368793.3 | ||
MTRF1 | ENST00000497679.6 | n.*228G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 | ENSP00000484414.1 | ||||
MTRF1 | ENST00000497679.6 | n.*228G>A | 3_prime_UTR_variant | Exon 5 of 6 | 3 | ENSP00000484414.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.565G>A (p.V189M) alteration is located in exon 4 (coding exon 3) of the MTRF1 gene. This alteration results from a G to A substitution at nucleotide position 565, causing the valine (V) at amino acid position 189 to be replaced by a methionine (M). 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