rs3816800
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024490.4(ATP10A):c.3894G>T(p.Arg1298Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,602,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Benignin ClinVar.
Frequency
Consequence
NM_024490.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP10A | NM_024490.4 | c.3894G>T | p.Arg1298Ser | missense_variant | 21/21 | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.3894G>T | p.Arg1298Ser | missense_variant | 21/21 | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151984Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000808 AC: 2AN: 247528Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134490
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1450278Hom.: 0 Cov.: 61 AF XY: 0.00000417 AC XY: 3AN XY: 719062
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at