14-103563003-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_001370595.2(COA8):āc.2T>Cā(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 0.00000321 in 1,557,840 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>C | 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>C | p.Met1? | start_lost | Exon 1 of 5 | 1 | NM_001370595.2 | ENSP00000386485.3 | ||
ENSG00000256500 | ENST00000472726.3 | c.2T>C | 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: 0.0000179 AC: 3AN: 167928Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 92424
GnomAD4 exome AF: 0.00000285 AC: 4AN: 1405704Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 695930
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.41T>C (p.M14T) alteration is located in exon 1 (coding exon 1) of the APOPT1 gene. This alteration results from a T to C substitution at nucleotide position 41, causing the methionine (M) at amino acid position 14 to be replaced by a threonine (T). 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