14-103563003-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_001370595.2(COA8):āc.2T>Gā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,557,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001370595.2 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COA8 | NM_001370595.2 | c.2T>G | p.Met1? | start_lost | Exon 1 of 5 | ENST00000409074.8 | NP_001357524.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COA8 | ENST00000409074.8 | c.2T>G | p.Met1? | start_lost | Exon 1 of 5 | 1 | NM_001370595.2 | ENSP00000386485.3 | ||
ENSG00000256500 | ENST00000472726.3 | c.2T>G | p.Met1? | start_lost | Exon 1 of 18 | 2 | ENSP00000439065.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000595 AC: 1AN: 167928Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 92424
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1405702Hom.: 0 Cov.: 32 AF XY: 0.00000144 AC XY: 1AN XY: 695930
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.41T>G (p.M14R) alteration is located in exon 1 (coding exon 1) of the APOPT1 gene. This alteration results from a T to G substitution at nucleotide position 41, causing the methionine (M) at amino acid position 14 to be replaced by an arginine (R). 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