chr15-25679366-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024490.4(ATP10A):c.4475G>A(p.Gly1492Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000881 in 1,589,876 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. Variant has been reported in ClinVar as Uncertain significance (★).
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.4475G>A | p.Gly1492Glu | missense_variant | 21/21 | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.4475G>A | p.Gly1492Glu | missense_variant | 21/21 | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152076Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246890Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133390
GnomAD4 exome AF: 0.00000417 AC: 6AN: 1437800Hom.: 0 Cov.: 29 AF XY: 0.00000282 AC XY: 2AN XY: 710288
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152076Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.4475G>A (p.G1492E) alteration is located in exon 21 (coding exon 21) of the ATP10A gene. This alteration results from a G to A substitution at nucleotide position 4475, causing the glycine (G) at amino acid position 1492 to be replaced by a glutamic acid (E). 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