20-59030421-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006886.4(ATP5F1E):c.41G>A(p.Arg14Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,613,560 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R14P) has been classified as Uncertain significance.
Frequency
Consequence
NM_006886.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP5F1E | NM_006886.4 | c.41G>A | p.Arg14Gln | missense_variant | Exon 2 of 3 | ENST00000243997.8 | NP_008817.1 | |
SLMO2-ATP5E | NR_037929.1 | n.745G>A | non_coding_transcript_exon_variant | Exon 7 of 8 | ||||
SLMO2-ATP5E | NR_037930.1 | n.486G>A | non_coding_transcript_exon_variant | Exon 5 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP5F1E | ENST00000243997.8 | c.41G>A | p.Arg14Gln | missense_variant | Exon 2 of 3 | 1 | NM_006886.4 | ENSP00000243997.3 | ||
ATP5F1E | ENST00000395659.1 | c.41G>A | p.Arg14Gln | missense_variant | Exon 2 of 2 | 1 | ENSP00000379019.1 | |||
ATP5F1E | ENST00000395663.1 | c.41G>A | p.Arg14Gln | missense_variant | Exon 2 of 3 | 2 | ENSP00000379023.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251422Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135882
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461404Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727020
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at