15-25679591-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024490.4(ATP10A):c.4250C>T(p.Ala1417Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,610,596 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.4250C>T | p.Ala1417Val | missense_variant | 21/21 | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.4250C>T | p.Ala1417Val | missense_variant | 21/21 | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135216
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1458280Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 724782
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74490
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 11, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at