chr15-25679762-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_024490.4(ATP10A):c.4079C>T(p.Pro1360Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,613,122 control chromosomes in the GnomAD database, including 5 homozygotes. 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP10A | NM_024490.4 | c.4079C>T | p.Pro1360Leu | missense_variant | 21/21 | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.4079C>T | p.Pro1360Leu | missense_variant | 21/21 | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000867 AC: 132AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000760 AC: 190AN: 250022Hom.: 1 AF XY: 0.000798 AC XY: 108AN XY: 135366
GnomAD4 exome AF: 0.00120 AC: 1748AN: 1460834Hom.: 5 Cov.: 32 AF XY: 0.00122 AC XY: 887AN XY: 726740
GnomAD4 genome ? AF: 0.000867 AC: 132AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.000712 AC XY: 53AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2021 | The c.4079C>T (p.P1360L) alteration is located in exon 21 (coding exon 21) of the ATP10A gene. This alteration results from a C to T substitution at nucleotide position 4079, causing the proline (P) at amino acid position 1360 to be replaced by a leucine (L). 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