chr3-11839223-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_001284401.2(TAMM41):c.410C>T(p.Pro137Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,608,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_001284401.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAMM41 | NM_001284401.2 | c.410C>T | p.Pro137Leu | missense_variant, splice_region_variant | 3/8 | ENST00000455809.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAMM41 | ENST00000455809.6 | c.410C>T | p.Pro137Leu | missense_variant, splice_region_variant | 3/8 | 3 | NM_001284401.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250668Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135428
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1456670Hom.: 0 Cov.: 29 AF XY: 0.0000193 AC XY: 14AN XY: 724812
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation deficiency 56 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 28, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at