chr15-25679625-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024490.4(ATP10A):c.4216C>A(p.Pro1406Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,022 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.4216C>A | p.Pro1406Thr | missense_variant | 21/21 | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.4216C>A | p.Pro1406Thr | missense_variant | 21/21 | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249288Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135170
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460854Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726698
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.4216C>A (p.P1406T) alteration is located in exon 21 (coding exon 21) of the ATP10A gene. This alteration results from a C to A substitution at nucleotide position 4216, causing the proline (P) at amino acid position 1406 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