15-25681057-C-T
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_024490.4(ATP10A):c.3510G>A(p.Thr1170Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,613,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000057 ( 0 hom. )
Consequence
ATP10A
NM_024490.4 synonymous
NM_024490.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.634
Genes affected
ATP10A (HGNC:13542): (ATPase phospholipid transporting 10A (putative)) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. This gene is maternally expressed. It maps within the most common interval of deletion responsible for Angelman syndrome, also known as 'happy puppet syndrome'. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP7
Synonymous conserved (PhyloP=-0.634 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ATP10A | NM_024490.4 | c.3510G>A | p.Thr1170Thr | synonymous_variant | 18/21 | ENST00000555815.7 | NP_077816.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ATP10A | ENST00000555815.7 | c.3510G>A | p.Thr1170Thr | synonymous_variant | 18/21 | 5 | NM_024490.4 | ENSP00000450480.2 |
Frequencies
GnomAD3 genomes 0.0000263 AC: 4AN: 152050Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250822Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135498
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GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461400Hom.: 0 Cov.: 36 AF XY: 0.0000619 AC XY: 45AN XY: 727034
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GnomAD4 genome 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74384
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Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at