chr15-25680111-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024490.4(ATP10A):c.3866+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000695 in 1,612,382 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00072 ( 1 hom. )
Consequence
ATP10A
NM_024490.4 intron
NM_024490.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.16
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 -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 15-25680111-C-T is Benign according to our data. Variant chr15-25680111-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 729418.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP10A | NM_024490.4 | c.3866+10G>A | intron_variant | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.3866+10G>A | intron_variant | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152182Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000463 AC: 116AN: 250384Hom.: 0 AF XY: 0.000436 AC XY: 59AN XY: 135274
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GnomAD4 exome AF: 0.000717 AC: 1047AN: 1460082Hom.: 1 Cov.: 33 AF XY: 0.000687 AC XY: 499AN XY: 726260
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 30, 2018 | - - |
Computational scores
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Benign
Cadd
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at