chr19-44892457-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001128917.2(TOMM40):c.339T>G(p.Phe113Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001128917.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOMM40 | NM_001128917.2 | c.339T>G | p.Phe113Leu | missense_variant | 2/9 | ENST00000426677.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOMM40 | ENST00000426677.7 | c.339T>G | p.Phe113Leu | missense_variant | 2/9 | 1 | NM_001128917.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151842Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 33
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151842Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74144
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at